Starting phenix.real_space_refine on Sun Mar 24 10:32:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpe_3535/03_2024/5mpe_3535.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpe_3535/03_2024/5mpe_3535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpe_3535/03_2024/5mpe_3535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpe_3535/03_2024/5mpe_3535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpe_3535/03_2024/5mpe_3535.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpe_3535/03_2024/5mpe_3535.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 151 5.16 5 C 26021 2.51 5 N 6810 2.21 5 O 7992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W GLU 4": "OE1" <-> "OE2" Residue "W GLU 14": "OE1" <-> "OE2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W GLU 148": "OE1" <-> "OE2" Residue "W GLU 152": "OE1" <-> "OE2" Residue "W GLU 167": "OE1" <-> "OE2" Residue "W TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 193": "OE1" <-> "OE2" Residue "W GLU 194": "OE1" <-> "OE2" Residue "V GLU 56": "OE1" <-> "OE2" Residue "V GLU 130": "OE1" <-> "OE2" Residue "V GLU 169": "OE1" <-> "OE2" Residue "V TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 232": "OE1" <-> "OE2" Residue "V GLU 249": "OE1" <-> "OE2" Residue "V GLU 257": "OE1" <-> "OE2" Residue "V GLU 258": "OE1" <-> "OE2" Residue "V GLU 263": "OE1" <-> "OE2" Residue "V GLU 264": "OE1" <-> "OE2" Residue "V GLU 265": "OE1" <-> "OE2" Residue "V GLU 282": "OE1" <-> "OE2" Residue "V GLU 289": "OE1" <-> "OE2" Residue "T ASP 49": "OD1" <-> "OD2" Residue "T PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 125": "OE1" <-> "OE2" Residue "T TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 154": "OE1" <-> "OE2" Residue "T PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 188": "OE1" <-> "OE2" Residue "T GLU 214": "OE1" <-> "OE2" Residue "T GLU 253": "OE1" <-> "OE2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 60": "OE1" <-> "OE2" Residue "X GLU 95": "OE1" <-> "OE2" Residue "X TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 103": "OE1" <-> "OE2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X GLU 120": "OE1" <-> "OE2" Residue "Y GLU 30": "OE1" <-> "OE2" Residue "Y GLU 31": "OE1" <-> "OE2" Residue "Y GLU 36": "OE1" <-> "OE2" Residue "Z GLU 14": "OE1" <-> "OE2" Residue "Z GLU 21": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z GLU 50": "OE1" <-> "OE2" Residue "Z GLU 54": "OE1" <-> "OE2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "Z GLU 65": "OE1" <-> "OE2" Residue "Z GLU 73": "OE1" <-> "OE2" Residue "Z TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 147": "OE1" <-> "OE2" Residue "Z GLU 160": "OE1" <-> "OE2" Residue "Z GLU 163": "OE1" <-> "OE2" Residue "Z GLU 170": "OE1" <-> "OE2" Residue "Z GLU 174": "OE1" <-> "OE2" Residue "Z GLU 198": "OE1" <-> "OE2" Residue "Z GLU 217": "OE1" <-> "OE2" Residue "Z GLU 218": "OE1" <-> "OE2" Residue "Z GLU 239": "OE1" <-> "OE2" Residue "Z GLU 290": "OE1" <-> "OE2" Residue "Z GLU 291": "OE1" <-> "OE2" Residue "Z GLU 322": "OE1" <-> "OE2" Residue "Z GLU 324": "OE1" <-> "OE2" Residue "Z GLU 337": "OE1" <-> "OE2" Residue "Z GLU 355": "OE1" <-> "OE2" Residue "Z ASP 363": "OD1" <-> "OD2" Residue "Z GLU 444": "OE1" <-> "OE2" Residue "Z GLU 521": "OE1" <-> "OE2" Residue "Z ASP 561": "OD1" <-> "OD2" Residue "Z GLU 579": "OE1" <-> "OE2" Residue "Z GLU 592": "OE1" <-> "OE2" Residue "Z GLU 600": "OE1" <-> "OE2" Residue "Z GLU 632": "OE1" <-> "OE2" Residue "Z GLU 704": "OE1" <-> "OE2" Residue "Z GLU 724": "OE1" <-> "OE2" Residue "Z GLU 725": "OE1" <-> "OE2" Residue "Z GLU 726": "OE1" <-> "OE2" Residue "Z GLU 729": "OE1" <-> "OE2" Residue "Z ASP 751": "OD1" <-> "OD2" Residue "Z TYR 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 841": "OE1" <-> "OE2" Residue "Z GLU 961": "OE1" <-> "OE2" Residue "Z GLU 964": "OE1" <-> "OE2" Residue "Z GLU 966": "OE1" <-> "OE2" Residue "N GLU 42": "OE1" <-> "OE2" Residue "N TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 138": "OE1" <-> "OE2" Residue "N GLU 142": "OE1" <-> "OE2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "N GLU 248": "OE1" <-> "OE2" Residue "N GLU 276": "OE1" <-> "OE2" Residue "N TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 394": "NH1" <-> "NH2" Residue "N ARG 417": "NH1" <-> "NH2" Residue "N GLU 429": "OE1" <-> "OE2" Residue "N GLU 464": "OE1" <-> "OE2" Residue "N GLU 479": "OE1" <-> "OE2" Residue "N GLU 507": "OE1" <-> "OE2" Residue "N GLU 530": "OE1" <-> "OE2" Residue "N ARG 786": "NH1" <-> "NH2" Residue "N GLU 789": "OE1" <-> "OE2" Residue "N GLU 790": "OE1" <-> "OE2" Residue "N GLU 795": "OE1" <-> "OE2" Residue "N GLU 797": "OE1" <-> "OE2" Residue "N GLU 820": "OE1" <-> "OE2" Residue "N PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 912": "OE1" <-> "OE2" Residue "S GLU 22": "OE1" <-> "OE2" Residue "S GLU 28": "OE1" <-> "OE2" Residue "S GLU 33": "OE1" <-> "OE2" Residue "S GLU 124": "OE1" <-> "OE2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S GLU 157": "OE1" <-> "OE2" Residue "S GLU 199": "OE1" <-> "OE2" Residue "S GLU 228": "OE1" <-> "OE2" Residue "S TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 263": "OD1" <-> "OD2" Residue "S GLU 291": "OE1" <-> "OE2" Residue "S GLU 416": "OE1" <-> "OE2" Residue "S TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 463": "OE1" <-> "OE2" Residue "S TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 483": "OE1" <-> "OE2" Residue "P ASP 31": "OD1" <-> "OD2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P GLU 77": "OE1" <-> "OE2" Residue "P TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 133": "OE1" <-> "OE2" Residue "P GLU 149": "OE1" <-> "OE2" Residue "P GLU 150": "OE1" <-> "OE2" Residue "P ASP 154": "OD1" <-> "OD2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P GLU 182": "OE1" <-> "OE2" Residue "P GLU 214": "OE1" <-> "OE2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "P GLU 236": "OE1" <-> "OE2" Residue "P ARG 310": "NH1" <-> "NH2" Residue "P GLU 319": "OE1" <-> "OE2" Residue "P GLU 332": "OE1" <-> "OE2" Residue "P GLU 339": "OE1" <-> "OE2" Residue "P GLU 355": "OE1" <-> "OE2" Residue "P ASP 370": "OD1" <-> "OD2" Residue "P GLU 403": "OE1" <-> "OE2" Residue "P GLU 414": "OE1" <-> "OE2" Residue "P GLU 424": "OE1" <-> "OE2" Residue "P GLU 437": "OE1" <-> "OE2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 164": "OE1" <-> "OE2" Residue "Q TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 289": "OE1" <-> "OE2" Residue "Q TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 322": "OE1" <-> "OE2" Residue "Q GLU 324": "OE1" <-> "OE2" Residue "Q PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 344": "OE1" <-> "OE2" Residue "Q GLU 352": "OE1" <-> "OE2" Residue "Q GLU 358": "OE1" <-> "OE2" Residue "Q GLU 374": "OE1" <-> "OE2" Residue "Q GLU 401": "OE1" <-> "OE2" Residue "Q GLU 428": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 41": "OE1" <-> "OE2" Residue "R GLU 57": "OE1" <-> "OE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 69": "OE1" <-> "OE2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R GLU 122": "OE1" <-> "OE2" Residue "R ASP 124": "OD1" <-> "OD2" Residue "R GLU 129": "OE1" <-> "OE2" Residue "R TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 192": "OE1" <-> "OE2" Residue "R GLU 226": "OE1" <-> "OE2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R GLU 310": "OE1" <-> "OE2" Residue "R TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R GLU 343": "OE1" <-> "OE2" Residue "R GLU 389": "OE1" <-> "OE2" Residue "U GLU 23": "OE1" <-> "OE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 141": "OE1" <-> "OE2" Residue "U GLU 151": "OE1" <-> "OE2" Residue "U PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 164": "OE1" <-> "OE2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "U GLU 246": "OE1" <-> "OE2" Residue "U GLU 272": "OE1" <-> "OE2" Residue "U GLU 293": "OE1" <-> "OE2" Residue "O GLU 17": "OE1" <-> "OE2" Residue "O ASP 51": "OD1" <-> "OD2" Residue "O TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 132": "OE1" <-> "OE2" Residue "O GLU 200": "OE1" <-> "OE2" Residue "O GLU 209": "OE1" <-> "OE2" Residue "O GLU 232": "OE1" <-> "OE2" Residue "O GLU 240": "OE1" <-> "OE2" Residue "O GLU 284": "OE1" <-> "OE2" Residue "O GLU 378": "OE1" <-> "OE2" Residue "O GLU 385": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40974 Number of models: 1 Model: "" Number of chains: 13 Chain: "W" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1534 Classifications: {'peptide': 197} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 187} Chain: "V" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2274 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 282} Chain: "T" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 7, 'TRANS': 258} Chain: "X" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1032 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "Y" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 435 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain breaks: 1 Chain: "Z" Number of atoms: 7005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7005 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 30, 'TRANS': 875} Chain breaks: 1 Chain: "N" Number of atoms: 6882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6882 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 23, 'TRANS': 866} Chain breaks: 1 Chain: "S" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3894 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 11, 'TRANS': 463} Chain: "P" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3608 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 9, 'TRANS': 430} Chain: "Q" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3499 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 425} Chain: "R" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3060 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 7, 'TRANS': 373} Chain breaks: 1 Chain: "U" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2373 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 288} Chain: "O" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3186 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 378} Time building chain proxies: 20.62, per 1000 atoms: 0.50 Number of scatterers: 40974 At special positions: 0 Unit cell: (231.84, 200.1, 218.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 151 16.00 O 7992 8.00 N 6810 7.00 C 26021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.31 Conformation dependent library (CDL) restraints added in 6.3 seconds 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9824 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 16 sheets defined 71.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'W' and resid 24 through 44 removed outlier: 4.138A pdb=" N ILE W 30 " --> pdb=" O PHE W 26 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER W 43 " --> pdb=" O ALA W 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN W 44 " --> pdb=" O LYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 78 removed outlier: 3.881A pdb=" N ILE W 72 " --> pdb=" O GLU W 68 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP W 78 " --> pdb=" O ALA W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 99 removed outlier: 3.554A pdb=" N ALA W 90 " --> pdb=" O HIS W 86 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN W 92 " --> pdb=" O ALA W 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU W 96 " --> pdb=" O GLN W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 135 removed outlier: 3.645A pdb=" N LEU W 125 " --> pdb=" O SER W 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS W 133 " --> pdb=" O ALA W 129 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS W 134 " --> pdb=" O LYS W 130 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN W 135 " --> pdb=" O THR W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 149 removed outlier: 3.540A pdb=" N GLU W 148 " --> pdb=" O GLY W 145 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN W 149 " --> pdb=" O GLU W 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 145 through 149' Processing helix chain 'W' and resid 153 through 162 removed outlier: 3.873A pdb=" N PHE W 157 " --> pdb=" O LEU W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 188 Processing helix chain 'V' and resid 30 through 45 removed outlier: 3.502A pdb=" N GLY V 44 " --> pdb=" O HIS V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 98 removed outlier: 3.696A pdb=" N GLN V 97 " --> pdb=" O ASP V 93 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR V 98 " --> pdb=" O MET V 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 133 removed outlier: 3.562A pdb=" N ASN V 124 " --> pdb=" O SER V 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE V 129 " --> pdb=" O THR V 125 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN V 131 " --> pdb=" O LYS V 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU V 132 " --> pdb=" O SER V 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 148 removed outlier: 3.789A pdb=" N VAL V 147 " --> pdb=" O ILE V 144 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS V 148 " --> pdb=" O GLN V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 166 removed outlier: 3.825A pdb=" N LEU V 164 " --> pdb=" O ASP V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 174 removed outlier: 3.718A pdb=" N THR V 174 " --> pdb=" O ARG V 171 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 194 Processing helix chain 'V' and resid 206 through 215 Processing helix chain 'V' and resid 229 through 255 removed outlier: 3.635A pdb=" N LYS V 233 " --> pdb=" O ASP V 229 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL V 245 " --> pdb=" O THR V 241 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS V 246 " --> pdb=" O LYS V 242 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN V 250 " --> pdb=" O LYS V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 270 Processing helix chain 'V' and resid 275 through 306 removed outlier: 3.545A pdb=" N ILE V 292 " --> pdb=" O LEU V 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 18 removed outlier: 4.074A pdb=" N SER T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU T 16 " --> pdb=" O SER T 12 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 41 removed outlier: 3.909A pdb=" N CYS T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU T 24 " --> pdb=" O TYR T 20 " (cutoff:3.500A) Proline residue: T 28 - end of helix removed outlier: 3.767A pdb=" N ILE T 32 " --> pdb=" O PRO T 28 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU T 33 " --> pdb=" O PRO T 29 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE T 35 " --> pdb=" O LYS T 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN T 37 " --> pdb=" O GLU T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 72 removed outlier: 4.261A pdb=" N ASN T 53 " --> pdb=" O ASP T 49 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP T 54 " --> pdb=" O ILE T 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE T 61 " --> pdb=" O ILE T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 91 removed outlier: 3.615A pdb=" N PHE T 78 " --> pdb=" O ASN T 74 " (cutoff:3.500A) Proline residue: T 87 - end of helix Processing helix chain 'T' and resid 99 through 116 Processing helix chain 'T' and resid 118 through 130 removed outlier: 3.803A pdb=" N SER T 124 " --> pdb=" O THR T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 133 No H-bonds generated for 'chain 'T' and resid 131 through 133' Processing helix chain 'T' and resid 142 through 155 removed outlier: 3.747A pdb=" N ILE T 146 " --> pdb=" O LEU T 142 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.510A pdb=" N LEU T 164 " --> pdb=" O ALA T 160 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN T 165 " --> pdb=" O TRP T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 170 No H-bonds generated for 'chain 'T' and resid 168 through 170' Processing helix chain 'T' and resid 174 through 197 removed outlier: 5.065A pdb=" N ILE T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS T 182 " --> pdb=" O THR T 178 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER T 183 " --> pdb=" O ASP T 179 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU T 194 " --> pdb=" O ALA T 190 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU T 195 " --> pdb=" O LYS T 191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) Processing helix chain 'T' and resid 201 through 210 Processing helix chain 'T' and resid 213 through 224 removed outlier: 3.552A pdb=" N GLU T 218 " --> pdb=" O GLU T 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 235 through 248 removed outlier: 4.077A pdb=" N SER T 239 " --> pdb=" O PHE T 235 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS T 240 " --> pdb=" O ASN T 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU T 248 " --> pdb=" O ASP T 244 " (cutoff:3.500A) Processing helix chain 'T' and resid 252 through 257 Processing helix chain 'T' and resid 258 through 271 removed outlier: 3.689A pdb=" N ALA T 263 " --> pdb=" O ILE T 259 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET T 264 " --> pdb=" O ILE T 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE T 268 " --> pdb=" O MET T 264 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER T 269 " --> pdb=" O ASP T 265 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE T 270 " --> pdb=" O TYR T 266 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 131 removed outlier: 3.503A pdb=" N TYR X 122 " --> pdb=" O ASP X 118 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS X 124 " --> pdb=" O GLU X 120 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN X 131 " --> pdb=" O GLY X 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 31 removed outlier: 4.406A pdb=" N GLU Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 42 removed outlier: 3.630A pdb=" N ILE Y 40 " --> pdb=" O GLU Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 71 through 88 removed outlier: 3.909A pdb=" N LEU Y 77 " --> pdb=" O PHE Y 73 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS Y 85 " --> pdb=" O LEU Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 19 removed outlier: 3.605A pdb=" N GLU Z 14 " --> pdb=" O GLN Z 10 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE Z 18 " --> pdb=" O GLU Z 14 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 34 Processing helix chain 'Z' and resid 35 through 42 removed outlier: 3.857A pdb=" N SER Z 39 " --> pdb=" O GLU Z 35 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU Z 40 " --> pdb=" O GLU Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 58 removed outlier: 3.579A pdb=" N GLU Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU Z 51 " --> pdb=" O THR Z 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU Z 52 " --> pdb=" O ASP Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 70 through 75 removed outlier: 4.481A pdb=" N SER Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 70 through 75' Processing helix chain 'Z' and resid 85 through 90 removed outlier: 3.599A pdb=" N LEU Z 89 " --> pdb=" O VAL Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 104 removed outlier: 4.097A pdb=" N ILE Z 102 " --> pdb=" O ASP Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 127 removed outlier: 3.537A pdb=" N SER Z 114 " --> pdb=" O ASN Z 110 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP Z 117 " --> pdb=" O SER Z 113 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL Z 118 " --> pdb=" O SER Z 114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 141 removed outlier: 3.601A pdb=" N LEU Z 135 " --> pdb=" O LYS Z 131 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Z 138 " --> pdb=" O SER Z 134 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU Z 139 " --> pdb=" O LEU Z 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 164 removed outlier: 5.014A pdb=" N ILE Z 154 " --> pdb=" O GLY Z 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU Z 157 " --> pdb=" O TYR Z 153 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Z 160 " --> pdb=" O HIS Z 156 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE Z 161 " --> pdb=" O LEU Z 157 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL Z 164 " --> pdb=" O GLU Z 160 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 170 removed outlier: 3.980A pdb=" N GLN Z 168 " --> pdb=" O VAL Z 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 188 removed outlier: 4.438A pdb=" N ALA Z 188 " --> pdb=" O ASP Z 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 185 through 188' Processing helix chain 'Z' and resid 189 through 203 removed outlier: 3.743A pdb=" N PHE Z 195 " --> pdb=" O SER Z 191 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU Z 198 " --> pdb=" O GLU Z 194 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Z 201 " --> pdb=" O LYS Z 197 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG Z 202 " --> pdb=" O GLU Z 198 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU Z 203 " --> pdb=" O ASP Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 216 removed outlier: 3.607A pdb=" N ASN Z 215 " --> pdb=" O PHE Z 211 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 232 removed outlier: 3.970A pdb=" N VAL Z 221 " --> pdb=" O GLU Z 217 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU Z 226 " --> pdb=" O ASP Z 222 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE Z 227 " --> pdb=" O LEU Z 223 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP Z 231 " --> pdb=" O ILE Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 237 through 252 removed outlier: 3.614A pdb=" N GLN Z 243 " --> pdb=" O GLU Z 239 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG Z 244 " --> pdb=" O ASN Z 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 275 removed outlier: 3.767A pdb=" N VAL Z 262 " --> pdb=" O PRO Z 258 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA Z 263 " --> pdb=" O PRO Z 259 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU Z 265 " --> pdb=" O ASP Z 261 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR Z 267 " --> pdb=" O ALA Z 263 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER Z 270 " --> pdb=" O LYS Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 277 through 289 removed outlier: 4.370A pdb=" N ALA Z 281 " --> pdb=" O GLU Z 277 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE Z 282 " --> pdb=" O LEU Z 278 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA Z 283 " --> pdb=" O THR Z 279 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU Z 284 " --> pdb=" O ASP Z 280 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL Z 286 " --> pdb=" O ILE Z 282 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG Z 287 " --> pdb=" O ALA Z 283 " (cutoff:3.500A) Processing helix chain 'Z' and resid 290 through 303 removed outlier: 3.682A pdb=" N ILE Z 294 " --> pdb=" O GLU Z 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL Z 297 " --> pdb=" O MET Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 308 through 321 removed outlier: 3.699A pdb=" N TYR Z 312 " --> pdb=" O LYS Z 308 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE Z 313 " --> pdb=" O GLN Z 309 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE Z 321 " --> pdb=" O GLN Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 325 through 332 removed outlier: 3.625A pdb=" N ILE Z 330 " --> pdb=" O VAL Z 326 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN Z 332 " --> pdb=" O ASP Z 328 " (cutoff:3.500A) Processing helix chain 'Z' and resid 333 through 339 removed outlier: 3.566A pdb=" N PHE Z 339 " --> pdb=" O LEU Z 335 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 350 removed outlier: 3.816A pdb=" N ASN Z 347 " --> pdb=" O ALA Z 343 " (cutoff:3.500A) Processing helix chain 'Z' and resid 351 through 366 removed outlier: 3.659A pdb=" N GLU Z 355 " --> pdb=" O PRO Z 351 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP Z 356 " --> pdb=" O LYS Z 352 " (cutoff:3.500A) Processing helix chain 'Z' and resid 378 through 391 removed outlier: 3.596A pdb=" N SER Z 384 " --> pdb=" O ASN Z 380 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN Z 387 " --> pdb=" O SER Z 383 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY Z 388 " --> pdb=" O SER Z 384 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN Z 391 " --> pdb=" O ASN Z 387 " (cutoff:3.500A) Processing helix chain 'Z' and resid 397 through 402 removed outlier: 3.781A pdb=" N VAL Z 401 " --> pdb=" O ASP Z 397 " (cutoff:3.500A) Processing helix chain 'Z' and resid 404 through 409 Processing helix chain 'Z' and resid 413 through 424 removed outlier: 3.597A pdb=" N SER Z 417 " --> pdb=" O ASP Z 413 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE Z 422 " --> pdb=" O ALA Z 418 " (cutoff:3.500A) Processing helix chain 'Z' and resid 425 through 427 No H-bonds generated for 'chain 'Z' and resid 425 through 427' Processing helix chain 'Z' and resid 432 through 441 removed outlier: 3.758A pdb=" N LEU Z 436 " --> pdb=" O GLY Z 432 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS Z 438 " --> pdb=" O GLN Z 434 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR Z 439 " --> pdb=" O GLN Z 435 " (cutoff:3.500A) Processing helix chain 'Z' and resid 444 through 459 removed outlier: 3.786A pdb=" N LYS Z 448 " --> pdb=" O GLU Z 444 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY Z 450 " --> pdb=" O GLU Z 446 " (cutoff:3.500A) Processing helix chain 'Z' and resid 469 through 480 removed outlier: 4.284A pdb=" N LEU Z 473 " --> pdb=" O PRO Z 469 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP Z 476 " --> pdb=" O LEU Z 472 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR Z 477 " --> pdb=" O LEU Z 473 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR Z 479 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN Z 480 " --> pdb=" O ASP Z 476 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 498 removed outlier: 3.904A pdb=" N LEU Z 493 " --> pdb=" O ALA Z 489 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE Z 497 " --> pdb=" O LEU Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 502 through 510 removed outlier: 3.648A pdb=" N LEU Z 508 " --> pdb=" O GLU Z 504 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU Z 509 " --> pdb=" O VAL Z 505 " (cutoff:3.500A) Processing helix chain 'Z' and resid 520 through 523 Processing helix chain 'Z' and resid 524 through 535 removed outlier: 3.705A pdb=" N LEU Z 528 " --> pdb=" O ALA Z 524 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Z 530 " --> pdb=" O ALA Z 526 " (cutoff:3.500A) Processing helix chain 'Z' and resid 543 through 556 removed outlier: 3.649A pdb=" N ASP Z 548 " --> pdb=" O THR Z 544 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA Z 555 " --> pdb=" O LEU Z 551 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE Z 556 " --> pdb=" O GLU Z 552 " (cutoff:3.500A) Processing helix chain 'Z' and resid 559 through 575 removed outlier: 3.796A pdb=" N VAL Z 563 " --> pdb=" O LYS Z 559 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE Z 565 " --> pdb=" O ASP Z 561 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR Z 574 " --> pdb=" O LEU Z 570 " (cutoff:3.500A) Processing helix chain 'Z' and resid 582 through 589 removed outlier: 3.991A pdb=" N GLU Z 586 " --> pdb=" O ASP Z 582 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR Z 587 " --> pdb=" O ASP Z 583 " (cutoff:3.500A) Processing helix chain 'Z' and resid 593 through 608 removed outlier: 3.542A pdb=" N SER Z 597 " --> pdb=" O HIS Z 593 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE Z 599 " --> pdb=" O MET Z 595 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL Z 601 " --> pdb=" O SER Z 597 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU Z 602 " --> pdb=" O ALA Z 598 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS Z 606 " --> pdb=" O LEU Z 602 " (cutoff:3.500A) Processing helix chain 'Z' and resid 614 through 635 removed outlier: 3.546A pdb=" N LEU Z 620 " --> pdb=" O LEU Z 616 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG Z 623 " --> pdb=" O ASP Z 619 " (cutoff:3.500A) Proline residue: Z 626 - end of helix Processing helix chain 'Z' and resid 701 through 727 removed outlier: 3.527A pdb=" N ASP Z 712 " --> pdb=" O GLY Z 708 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS Z 713 " --> pdb=" O LYS Z 709 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU Z 725 " --> pdb=" O ASN Z 721 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU Z 726 " --> pdb=" O ASP Z 722 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU Z 727 " --> pdb=" O ASP Z 723 " (cutoff:3.500A) Processing helix chain 'Z' and resid 728 through 750 removed outlier: 4.012A pdb=" N VAL Z 733 " --> pdb=" O GLU Z 729 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP Z 734 " --> pdb=" O ALA Z 730 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL Z 740 " --> pdb=" O LEU Z 736 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU Z 741 " --> pdb=" O ALA Z 737 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA Z 744 " --> pdb=" O VAL Z 740 " (cutoff:3.500A) Processing helix chain 'Z' and resid 750 through 769 removed outlier: 3.917A pdb=" N LYS Z 754 " --> pdb=" O GLU Z 750 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU Z 755 " --> pdb=" O ASP Z 751 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET Z 756 " --> pdb=" O ILE Z 752 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG Z 759 " --> pdb=" O GLU Z 755 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY Z 762 " --> pdb=" O LEU Z 758 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS Z 763 " --> pdb=" O ARG Z 759 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET Z 765 " --> pdb=" O PHE Z 761 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS Z 766 " --> pdb=" O GLY Z 762 " (cutoff:3.500A) Processing helix chain 'Z' and resid 775 through 787 removed outlier: 3.736A pdb=" N VAL Z 783 " --> pdb=" O ALA Z 779 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER Z 786 " --> pdb=" O ILE Z 782 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP Z 787 " --> pdb=" O VAL Z 783 " (cutoff:3.500A) Processing helix chain 'Z' and resid 790 through 800 removed outlier: 4.168A pdb=" N ASP Z 794 " --> pdb=" O MET Z 790 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG Z 798 " --> pdb=" O ASP Z 794 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE Z 799 " --> pdb=" O THR Z 795 " (cutoff:3.500A) Processing helix chain 'Z' and resid 806 through 822 removed outlier: 3.900A pdb=" N ASN Z 810 " --> pdb=" O GLU Z 806 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY Z 816 " --> pdb=" O ILE Z 812 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU Z 817 " --> pdb=" O PHE Z 813 " (cutoff:3.500A) Processing helix chain 'Z' and resid 825 through 840 removed outlier: 3.741A pdb=" N SER Z 836 " --> pdb=" O ARG Z 832 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG Z 840 " --> pdb=" O SER Z 836 " (cutoff:3.500A) Processing helix chain 'Z' and resid 864 through 869 removed outlier: 4.229A pdb=" N ASN Z 868 " --> pdb=" O MET Z 864 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP Z 869 " --> pdb=" O ASP Z 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 864 through 869' Processing helix chain 'Z' and resid 877 through 884 Processing helix chain 'N' and resid 6 through 15 Processing helix chain 'N' and resid 17 through 30 removed outlier: 3.748A pdb=" N LYS N 21 " --> pdb=" O GLN N 17 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR N 23 " --> pdb=" O SER N 19 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER N 27 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 41 removed outlier: 3.501A pdb=" N ASN N 41 " --> pdb=" O GLU N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 52 removed outlier: 3.620A pdb=" N TYR N 50 " --> pdb=" O ILE N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 73 Processing helix chain 'N' and resid 74 through 86 removed outlier: 3.556A pdb=" N ALA N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU N 83 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 94 Processing helix chain 'N' and resid 99 through 118 removed outlier: 3.554A pdb=" N GLN N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS N 115 " --> pdb=" O GLN N 111 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR N 118 " --> pdb=" O SER N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 148 removed outlier: 3.505A pdb=" N SER N 135 " --> pdb=" O PRO N 131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA N 147 " --> pdb=" O LYS N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 161 removed outlier: 3.637A pdb=" N ALA N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 173 removed outlier: 3.512A pdb=" N LEU N 170 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 197 removed outlier: 3.578A pdb=" N ASN N 182 " --> pdb=" O SER N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 217 removed outlier: 3.552A pdb=" N ARG N 203 " --> pdb=" O ASN N 199 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP N 212 " --> pdb=" O ARG N 208 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET N 217 " --> pdb=" O PHE N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 233 removed outlier: 3.589A pdb=" N LYS N 227 " --> pdb=" O LEU N 223 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL N 228 " --> pdb=" O THR N 224 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL N 229 " --> pdb=" O LEU N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 246 removed outlier: 3.571A pdb=" N ALA N 238 " --> pdb=" O ASP N 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN N 240 " --> pdb=" O GLY N 236 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU N 241 " --> pdb=" O LEU N 237 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 265 removed outlier: 3.805A pdb=" N SER N 263 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER N 264 " --> pdb=" O ASP N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 281 removed outlier: 3.544A pdb=" N LEU N 270 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 292 removed outlier: 4.019A pdb=" N LEU N 287 " --> pdb=" O ASP N 283 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE N 289 " --> pdb=" O ALA N 285 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY N 292 " --> pdb=" O ASN N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 307 Processing helix chain 'N' and resid 311 through 321 removed outlier: 3.570A pdb=" N ASN N 315 " --> pdb=" O ILE N 311 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS N 318 " --> pdb=" O LEU N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 340 Processing helix chain 'N' and resid 346 through 352 removed outlier: 3.531A pdb=" N ALA N 351 " --> pdb=" O SER N 347 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 358 removed outlier: 3.520A pdb=" N LYS N 358 " --> pdb=" O PRO N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 361 through 375 removed outlier: 3.700A pdb=" N PHE N 365 " --> pdb=" O ASN N 361 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU N 371 " --> pdb=" O ALA N 367 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY N 372 " --> pdb=" O THR N 368 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL N 373 " --> pdb=" O ALA N 369 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE N 374 " --> pdb=" O SER N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 378 through 387 removed outlier: 4.366A pdb=" N LYS N 383 " --> pdb=" O LEU N 379 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS N 384 " --> pdb=" O LEU N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 397 through 413 removed outlier: 3.716A pdb=" N LYS N 401 " --> pdb=" O SER N 397 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU N 405 " --> pdb=" O LYS N 401 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU N 408 " --> pdb=" O SER N 404 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY N 409 " --> pdb=" O LEU N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 418 through 430 removed outlier: 4.147A pdb=" N TYR N 422 " --> pdb=" O ASP N 418 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU N 423 " --> pdb=" O THR N 419 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE N 426 " --> pdb=" O TYR N 422 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN N 430 " --> pdb=" O ILE N 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 454 removed outlier: 3.992A pdb=" N VAL N 441 " --> pdb=" O GLU N 437 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU N 442 " --> pdb=" O ASP N 438 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY N 445 " --> pdb=" O VAL N 441 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 473 removed outlier: 3.803A pdb=" N VAL N 469 " --> pdb=" O ALA N 465 " (cutoff:3.500A) Processing helix chain 'N' and resid 476 through 489 removed outlier: 3.762A pdb=" N ALA N 480 " --> pdb=" O THR N 476 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY N 486 " --> pdb=" O ALA N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 508 removed outlier: 4.204A pdb=" N GLN N 506 " --> pdb=" O PHE N 502 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU N 507 " --> pdb=" O THR N 503 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR N 508 " --> pdb=" O TYR N 504 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 525 removed outlier: 3.614A pdb=" N THR N 514 " --> pdb=" O HIS N 510 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA N 522 " --> pdb=" O ALA N 518 " (cutoff:3.500A) Processing helix chain 'N' and resid 528 through 531 Processing helix chain 'N' and resid 532 through 542 Processing helix chain 'N' and resid 544 through 559 removed outlier: 3.555A pdb=" N GLY N 550 " --> pdb=" O LEU N 546 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE N 553 " --> pdb=" O TYR N 549 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE N 555 " --> pdb=" O GLY N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 578 Processing helix chain 'N' and resid 580 through 595 removed outlier: 3.745A pdb=" N VAL N 588 " --> pdb=" O ARG N 584 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU N 591 " --> pdb=" O ALA N 587 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY N 592 " --> pdb=" O VAL N 588 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE N 593 " --> pdb=" O ILE N 589 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL N 594 " --> pdb=" O ALA N 590 " (cutoff:3.500A) Processing helix chain 'N' and resid 601 through 606 Processing helix chain 'N' and resid 606 through 612 Processing helix chain 'N' and resid 614 through 629 removed outlier: 3.527A pdb=" N PHE N 623 " --> pdb=" O CYS N 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 634 through 646 removed outlier: 3.704A pdb=" N ILE N 638 " --> pdb=" O LEU N 634 " (cutoff:3.500A) Proline residue: N 643 - end of helix removed outlier: 4.017A pdb=" N LYS N 646 " --> pdb=" O ASP N 642 " (cutoff:3.500A) Processing helix chain 'N' and resid 649 through 664 removed outlier: 3.546A pdb=" N ARG N 653 " --> pdb=" O VAL N 649 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER N 661 " --> pdb=" O MET N 657 " (cutoff:3.500A) Processing helix chain 'N' and resid 673 through 688 removed outlier: 3.901A pdb=" N ASP N 677 " --> pdb=" O PRO N 673 " (cutoff:3.500A) Processing helix chain 'N' and resid 692 through 707 removed outlier: 3.504A pdb=" N LYS N 696 " --> pdb=" O GLU N 692 " (cutoff:3.500A) Processing helix chain 'N' and resid 708 through 711 Processing helix chain 'N' and resid 726 through 738 removed outlier: 3.649A pdb=" N VAL N 730 " --> pdb=" O ASP N 726 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL N 731 " --> pdb=" O THR N 727 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN N 738 " --> pdb=" O VAL N 734 " (cutoff:3.500A) Processing helix chain 'N' and resid 742 through 751 removed outlier: 3.731A pdb=" N LEU N 745 " --> pdb=" O TRP N 742 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS N 747 " --> pdb=" O PRO N 744 " (cutoff:3.500A) Processing helix chain 'N' and resid 779 through 783 removed outlier: 3.794A pdb=" N PHE N 782 " --> pdb=" O GLU N 779 " (cutoff:3.500A) Processing helix chain 'N' and resid 789 through 821 removed outlier: 3.605A pdb=" N VAL N 796 " --> pdb=" O SER N 792 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU N 797 " --> pdb=" O GLY N 793 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER N 805 " --> pdb=" O THR N 801 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA N 810 " --> pdb=" O THR N 806 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS N 811 " --> pdb=" O THR N 807 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG N 813 " --> pdb=" O ARG N 809 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA N 814 " --> pdb=" O ALA N 810 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR N 817 " --> pdb=" O ARG N 813 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU N 820 " --> pdb=" O LYS N 816 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS N 821 " --> pdb=" O THR N 817 " (cutoff:3.500A) Processing helix chain 'N' and resid 875 through 880 removed outlier: 3.952A pdb=" N ARG N 880 " --> pdb=" O PRO N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 919 through 925 removed outlier: 4.220A pdb=" N MET N 923 " --> pdb=" O THR N 919 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 42 Processing helix chain 'S' and resid 47 through 65 removed outlier: 3.609A pdb=" N ASP S 59 " --> pdb=" O ARG S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 79 Processing helix chain 'S' and resid 84 through 96 removed outlier: 3.606A pdb=" N ILE S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 126 removed outlier: 3.641A pdb=" N GLU S 124 " --> pdb=" O SER S 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS S 125 " --> pdb=" O VAL S 121 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS S 126 " --> pdb=" O ASN S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 150 Processing helix chain 'S' and resid 152 through 168 removed outlier: 3.618A pdb=" N VAL S 156 " --> pdb=" O LEU S 152 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU S 157 " --> pdb=" O GLU S 153 " (cutoff:3.500A) Proline residue: S 165 - end of helix Processing helix chain 'S' and resid 173 through 198 removed outlier: 3.791A pdb=" N ILE S 179 " --> pdb=" O SER S 175 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS S 182 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU S 183 " --> pdb=" O ILE S 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR S 186 " --> pdb=" O LYS S 182 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU S 194 " --> pdb=" O SER S 190 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER S 198 " --> pdb=" O LEU S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 224 removed outlier: 3.862A pdb=" N ASP S 204 " --> pdb=" O GLU S 200 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE S 208 " --> pdb=" O ASP S 204 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE S 209 " --> pdb=" O ASN S 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE S 220 " --> pdb=" O LYS S 216 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER S 222 " --> pdb=" O LEU S 218 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU S 223 " --> pdb=" O LYS S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 245 removed outlier: 3.515A pdb=" N LYS S 230 " --> pdb=" O ASP S 226 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN S 244 " --> pdb=" O ASP S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 246 through 255 removed outlier: 3.687A pdb=" N SER S 255 " --> pdb=" O SER S 251 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 283 removed outlier: 3.566A pdb=" N ARG S 271 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE S 282 " --> pdb=" O LYS S 278 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN S 283 " --> pdb=" O ILE S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 300 removed outlier: 3.889A pdb=" N GLU S 291 " --> pdb=" O SER S 287 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE S 297 " --> pdb=" O ILE S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 325 Processing helix chain 'S' and resid 330 through 336 removed outlier: 3.655A pdb=" N HIS S 334 " --> pdb=" O LEU S 330 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 355 removed outlier: 3.739A pdb=" N HIS S 347 " --> pdb=" O LEU S 343 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 367 removed outlier: 3.592A pdb=" N PHE S 360 " --> pdb=" O ASP S 356 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR S 365 " --> pdb=" O THR S 361 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 374 removed outlier: 3.665A pdb=" N LYS S 373 " --> pdb=" O GLN S 369 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP S 374 " --> pdb=" O LEU S 370 " (cutoff:3.500A) Processing helix chain 'S' and resid 376 through 399 removed outlier: 3.748A pdb=" N ARG S 382 " --> pdb=" O GLN S 378 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG S 384 " --> pdb=" O CYS S 380 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER S 385 " --> pdb=" O VAL S 381 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN S 386 " --> pdb=" O ARG S 382 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL S 387 " --> pdb=" O LEU S 383 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE S 388 " --> pdb=" O ARG S 384 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 removed outlier: 3.582A pdb=" N CYS S 408 " --> pdb=" O LEU S 404 " (cutoff:3.500A) Processing helix chain 'S' and resid 415 through 430 removed outlier: 3.553A pdb=" N VAL S 419 " --> pdb=" O SER S 415 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG S 428 " --> pdb=" O SER S 424 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP S 429 " --> pdb=" O ARG S 425 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 489 removed outlier: 3.773A pdb=" N GLN S 459 " --> pdb=" O GLU S 455 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU S 463 " --> pdb=" O GLN S 459 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG S 464 " --> pdb=" O VAL S 460 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN S 469 " --> pdb=" O ILE S 465 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET S 479 " --> pdb=" O TYR S 475 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG S 480 " --> pdb=" O LEU S 476 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR S 481 " --> pdb=" O VAL S 477 " (cutoff:3.500A) Proline residue: S 482 - end of helix removed outlier: 3.773A pdb=" N LYS S 485 " --> pdb=" O TYR S 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 20 removed outlier: 4.287A pdb=" N LYS P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 29 removed outlier: 3.663A pdb=" N GLN P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 43 removed outlier: 4.017A pdb=" N ALA P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 68 removed outlier: 3.519A pdb=" N ALA P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS P 56 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 79 removed outlier: 3.990A pdb=" N LEU P 75 " --> pdb=" O LYS P 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN P 76 " --> pdb=" O TRP P 72 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU P 77 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU P 79 " --> pdb=" O LEU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 86 removed outlier: 3.780A pdb=" N HIS P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 108 removed outlier: 3.982A pdb=" N TYR P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN P 98 " --> pdb=" O GLN P 94 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS P 108 " --> pdb=" O LEU P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 Processing helix chain 'P' and resid 131 through 150 removed outlier: 4.322A pdb=" N GLU P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG P 138 " --> pdb=" O VAL P 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS P 141 " --> pdb=" O ALA P 137 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP P 142 " --> pdb=" O ARG P 138 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU P 150 " --> pdb=" O ILE P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 164 removed outlier: 3.648A pdb=" N ALA P 157 " --> pdb=" O ILE P 153 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP P 158 " --> pdb=" O ASP P 154 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 159 " --> pdb=" O GLU P 155 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN P 164 " --> pdb=" O LEU P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.659A pdb=" N LEU P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 201 removed outlier: 3.600A pdb=" N ALA P 196 " --> pdb=" O ASP P 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL P 198 " --> pdb=" O SER P 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG P 201 " --> pdb=" O THR P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 210 removed outlier: 3.662A pdb=" N LYS P 209 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN P 210 " --> pdb=" O THR P 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 206 through 210' Processing helix chain 'P' and resid 213 through 231 Processing helix chain 'P' and resid 233 through 247 removed outlier: 3.777A pdb=" N VAL P 237 " --> pdb=" O GLU P 233 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR P 247 " --> pdb=" O GLU P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 253 Processing helix chain 'P' and resid 253 through 271 Proline residue: P 259 - end of helix Processing helix chain 'P' and resid 274 through 287 removed outlier: 3.816A pdb=" N ASN P 278 " --> pdb=" O GLY P 274 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP P 279 " --> pdb=" O ASN P 275 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS P 283 " --> pdb=" O ASP P 279 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP P 287 " --> pdb=" O LYS P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 288 through 293 removed outlier: 3.548A pdb=" N LYS P 292 " --> pdb=" O ASN P 289 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 304 removed outlier: 3.808A pdb=" N LEU P 299 " --> pdb=" O SER P 295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL P 300 " --> pdb=" O GLN P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 319 removed outlier: 4.113A pdb=" N LYS P 316 " --> pdb=" O PRO P 312 " (cutoff:3.500A) Processing helix chain 'P' and resid 331 through 339 removed outlier: 3.812A pdb=" N HIS P 336 " --> pdb=" O GLU P 332 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS P 337 " --> pdb=" O ALA P 333 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU P 339 " --> pdb=" O LYS P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 356 removed outlier: 3.694A pdb=" N GLU P 355 " --> pdb=" O ARG P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 370 Processing helix chain 'P' and resid 372 through 387 Processing helix chain 'P' and resid 407 through 440 removed outlier: 3.652A pdb=" N LEU P 411 " --> pdb=" O ASN P 407 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU P 427 " --> pdb=" O LEU P 423 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS P 435 " --> pdb=" O HIS P 431 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU P 437 " --> pdb=" O ILE P 433 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE P 438 " --> pdb=" O THR P 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 16 Processing helix chain 'Q' and resid 19 through 39 removed outlier: 3.705A pdb=" N ALA Q 23 " --> pdb=" O GLN Q 19 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN Q 25 " --> pdb=" O ASN Q 21 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 66 removed outlier: 3.653A pdb=" N GLU Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 78 removed outlier: 3.594A pdb=" N GLU Q 76 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE Q 77 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE Q 78 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 89 removed outlier: 3.698A pdb=" N MET Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA Q 89 " --> pdb=" O MET Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 107 Processing helix chain 'Q' and resid 109 through 124 removed outlier: 4.610A pdb=" N ASP Q 113 " --> pdb=" O ASP Q 109 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN Q 114 " --> pdb=" O SER Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 148 removed outlier: 4.051A pdb=" N SER Q 136 " --> pdb=" O PHE Q 132 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS Q 140 " --> pdb=" O SER Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 162 removed outlier: 3.808A pdb=" N SER Q 154 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU Q 157 " --> pdb=" O ASP Q 153 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE Q 158 " --> pdb=" O SER Q 154 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Q 161 " --> pdb=" O LEU Q 157 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU Q 162 " --> pdb=" O ILE Q 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 188 removed outlier: 4.020A pdb=" N VAL Q 175 " --> pdb=" O LYS Q 171 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS Q 178 " --> pdb=" O LEU Q 174 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS Q 183 " --> pdb=" O LEU Q 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 205 Processing helix chain 'Q' and resid 211 through 229 removed outlier: 3.604A pdb=" N VAL Q 215 " --> pdb=" O PRO Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 249 Processing helix chain 'Q' and resid 254 through 273 removed outlier: 3.970A pdb=" N LYS Q 269 " --> pdb=" O MET Q 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 282 removed outlier: 4.007A pdb=" N LYS Q 279 " --> pdb=" O ILE Q 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Q 282 " --> pdb=" O VAL Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 291 removed outlier: 3.863A pdb=" N TYR Q 291 " --> pdb=" O THR Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 309 removed outlier: 3.850A pdb=" N ASP Q 297 " --> pdb=" O SER Q 293 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS Q 300 " --> pdb=" O ILE Q 296 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU Q 304 " --> pdb=" O LYS Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 320 removed outlier: 3.545A pdb=" N PHE Q 314 " --> pdb=" O SER Q 310 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN Q 320 " --> pdb=" O THR Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 328 Processing helix chain 'Q' and resid 328 through 352 removed outlier: 3.530A pdb=" N ARG Q 332 " --> pdb=" O ASP Q 328 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 367 removed outlier: 3.822A pdb=" N ILE Q 365 " --> pdb=" O HIS Q 361 " (cutoff:3.500A) Processing helix chain 'Q' and resid 369 through 384 removed outlier: 3.758A pdb=" N GLN Q 379 " --> pdb=" O GLY Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 432 removed outlier: 3.841A pdb=" N ASP Q 410 " --> pdb=" O ASP Q 406 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS Q 421 " --> pdb=" O GLY Q 417 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU Q 428 " --> pdb=" O ASP Q 424 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL Q 432 " --> pdb=" O GLU Q 428 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 434 No H-bonds generated for 'chain 'Q' and resid 433 through 434' Processing helix chain 'R' and resid 20 through 20 No H-bonds generated for 'chain 'R' and resid 20 through 20' Processing helix chain 'R' and resid 21 through 35 removed outlier: 4.980A pdb=" N SER R 27 " --> pdb=" O ASN R 23 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 58 removed outlier: 3.569A pdb=" N ALA R 47 " --> pdb=" O ARG R 43 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 69 removed outlier: 3.570A pdb=" N LYS R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR R 65 " --> pdb=" O PRO R 61 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU R 68 " --> pdb=" O LYS R 64 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 123 removed outlier: 3.598A pdb=" N GLU R 115 " --> pdb=" O LYS R 111 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU R 122 " --> pdb=" O GLN R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 145 Processing helix chain 'R' and resid 146 through 160 removed outlier: 3.867A pdb=" N ALA R 150 " --> pdb=" O ASP R 146 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS R 152 " --> pdb=" O ASP R 148 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR R 153 " --> pdb=" O ASN R 149 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS R 156 " --> pdb=" O LYS R 152 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER R 157 " --> pdb=" O THR R 153 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS R 160 " --> pdb=" O LYS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 182 removed outlier: 3.531A pdb=" N ASP R 169 " --> pdb=" O GLY R 165 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY R 178 " --> pdb=" O ILE R 174 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE R 180 " --> pdb=" O ARG R 176 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 202 removed outlier: 3.785A pdb=" N VAL R 187 " --> pdb=" O ASP R 183 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU R 189 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS R 190 " --> pdb=" O TYR R 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL R 194 " --> pdb=" O LYS R 190 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 197 " --> pdb=" O ALA R 193 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU R 199 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 221 removed outlier: 3.842A pdb=" N ARG R 209 " --> pdb=" O GLU R 205 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL R 221 " --> pdb=" O HIS R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 234 removed outlier: 3.952A pdb=" N LYS R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP R 233 " --> pdb=" O LYS R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 removed outlier: 3.510A pdb=" N PHE R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 270 Processing helix chain 'R' and resid 273 through 279 removed outlier: 3.895A pdb=" N LEU R 277 " --> pdb=" O SER R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 Processing helix chain 'R' and resid 303 through 315 Processing helix chain 'R' and resid 325 through 344 removed outlier: 3.814A pdb=" N ARG R 331 " --> pdb=" O ASP R 327 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER R 344 " --> pdb=" O GLN R 340 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 358 Processing helix chain 'R' and resid 360 through 375 removed outlier: 3.798A pdb=" N LYS R 370 " --> pdb=" O ASN R 366 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Proline residue: R 373 - end of helix Processing helix chain 'R' and resid 395 through 424 removed outlier: 3.501A pdb=" N LYS R 405 " --> pdb=" O HIS R 401 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS R 413 " --> pdb=" O GLY R 409 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU R 423 " --> pdb=" O ALA R 419 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR R 424 " --> pdb=" O ALA R 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 25 removed outlier: 3.719A pdb=" N LEU U 15 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR U 22 " --> pdb=" O ALA U 18 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 84 removed outlier: 4.086A pdb=" N GLU U 74 " --> pdb=" O HIS U 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN U 75 " --> pdb=" O ASN U 71 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET U 79 " --> pdb=" O ASN U 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS U 82 " --> pdb=" O GLU U 78 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE U 83 " --> pdb=" O MET U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 114 removed outlier: 3.758A pdb=" N ILE U 106 " --> pdb=" O SER U 102 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU U 108 " --> pdb=" O LEU U 104 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU U 109 " --> pdb=" O LYS U 105 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE U 110 " --> pdb=" O ILE U 106 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR U 113 " --> pdb=" O LEU U 109 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 175 Processing helix chain 'U' and resid 185 through 215 removed outlier: 3.729A pdb=" N LEU U 194 " --> pdb=" O LEU U 190 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS U 203 " --> pdb=" O GLY U 199 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP U 212 " --> pdb=" O VAL U 208 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS U 213 " --> pdb=" O GLU U 209 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE U 215 " --> pdb=" O LEU U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 235 removed outlier: 3.947A pdb=" N LEU U 226 " --> pdb=" O ASN U 222 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP U 231 " --> pdb=" O GLY U 227 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL U 232 " --> pdb=" O LYS U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 298 removed outlier: 3.714A pdb=" N ASP U 245 " --> pdb=" O THR U 241 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR U 266 " --> pdb=" O GLN U 262 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL U 267 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS U 268 " --> pdb=" O ALA U 264 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE U 285 " --> pdb=" O LEU U 281 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU U 291 " --> pdb=" O ALA U 287 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE U 292 " --> pdb=" O PHE U 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 18 Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.660A pdb=" N PHE O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU O 27 " --> pdb=" O HIS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 49 removed outlier: 3.557A pdb=" N GLU O 43 " --> pdb=" O PHE O 39 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU O 45 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE O 48 " --> pdb=" O SER O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 68 removed outlier: 3.830A pdb=" N ARG O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 88 removed outlier: 3.771A pdb=" N VAL O 78 " --> pdb=" O ASN O 74 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 118 removed outlier: 3.535A pdb=" N LYS O 97 " --> pdb=" O ASP O 93 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN O 107 " --> pdb=" O LYS O 103 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER O 111 " --> pdb=" O GLN O 107 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG O 115 " --> pdb=" O SER O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 139 removed outlier: 4.298A pdb=" N ILE O 126 " --> pdb=" O HIS O 122 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU O 127 " --> pdb=" O GLY O 123 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU O 139 " --> pdb=" O ARG O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 160 removed outlier: 3.590A pdb=" N LYS O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 183 removed outlier: 4.137A pdb=" N THR O 168 " --> pdb=" O PRO O 164 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS O 182 " --> pdb=" O TYR O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 198 removed outlier: 4.139A pdb=" N TYR O 190 " --> pdb=" O ASN O 186 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR O 191 " --> pdb=" O SER O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 223 removed outlier: 3.503A pdb=" N LEU O 223 " --> pdb=" O ILE O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 235 removed outlier: 3.967A pdb=" N LEU O 234 " --> pdb=" O PHE O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 241 Processing helix chain 'O' and resid 245 through 248 Processing helix chain 'O' and resid 249 through 261 removed outlier: 3.589A pdb=" N VAL O 260 " --> pdb=" O ASN O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 277 removed outlier: 3.543A pdb=" N PHE O 266 " --> pdb=" O ASP O 262 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 278 through 283 Processing helix chain 'O' and resid 283 through 303 removed outlier: 4.229A pdb=" N ILE O 291 " --> pdb=" O LEU O 287 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS O 292 " --> pdb=" O ARG O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 318 Processing helix chain 'O' and resid 321 through 335 removed outlier: 3.893A pdb=" N GLU O 325 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS O 326 " --> pdb=" O ASP O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 387 removed outlier: 3.630A pdb=" N THR O 364 " --> pdb=" O GLY O 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS O 367 " --> pdb=" O ILE O 363 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS O 383 " --> pdb=" O LYS O 379 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET O 384 " --> pdb=" O LEU O 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 61 through 66 removed outlier: 7.298A pdb=" N LEU W 62 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N SER W 53 " --> pdb=" O LEU W 62 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR W 64 " --> pdb=" O LEU W 51 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU W 51 " --> pdb=" O THR W 64 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU W 4 " --> pdb=" O THR W 48 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY W 50 " --> pdb=" O GLU W 4 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR W 6 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE W 52 " --> pdb=" O THR W 6 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU W 8 " --> pdb=" O ILE W 52 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG W 109 " --> pdb=" O ALA W 5 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL W 9 " --> pdb=" O VAL W 111 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN W 108 " --> pdb=" O ALA W 138 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASP W 140 " --> pdb=" O GLN W 108 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE W 110 " --> pdb=" O ASP W 140 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE W 142 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA W 112 " --> pdb=" O ILE W 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 196 through 198 removed outlier: 3.700A pdb=" N VAL V 137 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL V 104 " --> pdb=" O GLY V 55 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLY V 55 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL V 49 " --> pdb=" O SER V 110 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE V 69 " --> pdb=" O LEU V 52 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU V 56 " --> pdb=" O VAL V 65 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL V 65 " --> pdb=" O GLU V 56 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL V 58 " --> pdb=" O VAL V 63 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL V 63 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL V 63 " --> pdb=" O THR V 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 8 through 10 removed outlier: 3.918A pdb=" N ILE X 8 " --> pdb=" O ILE X 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE X 35 " --> pdb=" O ILE X 8 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU X 49 " --> pdb=" O GLU X 34 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS X 36 " --> pdb=" O ASP X 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 13 through 15 removed outlier: 4.264A pdb=" N PHE X 98 " --> pdb=" O CYS X 15 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR X 97 " --> pdb=" O LEU X 89 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU X 89 " --> pdb=" O TYR X 97 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 894 through 895 removed outlier: 3.754A pdb=" N THR Z 967 " --> pdb=" O LEU Z 895 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU Z 966 " --> pdb=" O VAL Z 955 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 927 through 929 Processing sheet with id=AA7, first strand: chain 'N' and resid 713 through 715 Processing sheet with id=AA8, first strand: chain 'N' and resid 872 through 873 removed outlier: 4.481A pdb=" N THR N 872 " --> pdb=" O VAL N 758 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL N 758 " --> pdb=" O THR N 872 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL N 903 " --> pdb=" O THR N 757 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE N 759 " --> pdb=" O VAL N 903 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU N 905 " --> pdb=" O ILE N 759 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE N 761 " --> pdb=" O LEU N 905 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 768 through 769 removed outlier: 3.740A pdb=" N ILE N 768 " --> pdb=" O ILE N 917 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 865 through 869 Processing sheet with id=AB2, first strand: chain 'S' and resid 401 through 403 Processing sheet with id=AB3, first strand: chain 'P' and resid 391 through 392 removed outlier: 4.810A pdb=" N SER P 358 " --> pdb=" O PHE P 402 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR P 357 " --> pdb=" O GLY O 339 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE O 341 " --> pdb=" O TYR P 357 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS O 338 " --> pdb=" O SER O 351 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU O 308 " --> pdb=" O VAL O 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 357 through 358 removed outlier: 3.535A pdb=" N VAL Q 357 " --> pdb=" O LEU Q 397 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 347 through 349 removed outlier: 3.502A pdb=" N ILE R 387 " --> pdb=" O ASP R 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 7 through 10 removed outlier: 5.394A pdb=" N VAL U 48 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP U 40 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY U 91 " --> pdb=" O ILE U 37 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY U 39 " --> pdb=" O LEU U 89 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU U 89 " --> pdb=" O GLY U 39 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N LEU U 119 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE U 90 " --> pdb=" O LEU U 119 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU U 121 " --> pdb=" O ILE U 90 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TRP U 92 " --> pdb=" O LEU U 121 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL U 123 " --> pdb=" O TRP U 92 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS U 94 " --> pdb=" O VAL U 123 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA U 136 " --> pdb=" O LEU U 157 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL U 138 " --> pdb=" O LEU U 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 57 through 58 removed outlier: 3.687A pdb=" N GLU U 57 " --> pdb=" O PHE U 67 " (cutoff:3.500A) 2182 hydrogen bonds defined for protein. 6453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.65 Time building geometry restraints manager: 17.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.22: 1719 1.22 - 1.44: 17195 1.44 - 1.65: 22480 1.65 - 1.87: 249 1.87 - 2.09: 19 Bond restraints: 41662 Sorted by residual: bond pdb=" CZ TYR R 99 " pdb=" OH TYR R 99 " ideal model delta sigma weight residual 1.376 2.041 -0.665 2.10e-02 2.27e+03 1.00e+03 bond pdb=" C GLN P 78 " pdb=" N LEU P 79 " ideal model delta sigma weight residual 1.332 1.754 -0.421 1.40e-02 5.10e+03 9.05e+02 bond pdb=" CE1 TYR R 99 " pdb=" CZ TYR R 99 " ideal model delta sigma weight residual 1.378 2.089 -0.711 2.40e-02 1.74e+03 8.77e+02 bond pdb=" CA ASP S 59 " pdb=" CB ASP S 59 " ideal model delta sigma weight residual 1.529 1.098 0.431 1.55e-02 4.16e+03 7.72e+02 bond pdb=" CA THR S 127 " pdb=" CB THR S 127 " ideal model delta sigma weight residual 1.532 1.984 -0.452 1.65e-02 3.67e+03 7.51e+02 ... (remaining 41657 not shown) Histogram of bond angle deviations from ideal: 51.30 - 71.48: 1 71.48 - 91.65: 9 91.65 - 111.82: 16614 111.82 - 131.99: 39539 131.99 - 152.16: 116 Bond angle restraints: 56279 Sorted by residual: angle pdb=" CE1 TYR R 99 " pdb=" CZ TYR R 99 " pdb=" OH TYR R 99 " ideal model delta sigma weight residual 119.90 51.30 68.60 3.00e+00 1.11e-01 5.23e+02 angle pdb=" C TYR O 62 " pdb=" CA TYR O 62 " pdb=" CB TYR O 62 " ideal model delta sigma weight residual 110.81 78.61 32.20 1.60e+00 3.91e-01 4.05e+02 angle pdb=" C PHE Q 77 " pdb=" N ILE Q 78 " pdb=" CA ILE Q 78 " ideal model delta sigma weight residual 120.24 131.35 -11.11 6.30e-01 2.52e+00 3.11e+02 angle pdb=" O GLN P 78 " pdb=" C GLN P 78 " pdb=" N LEU P 79 " ideal model delta sigma weight residual 122.59 99.48 23.11 1.33e+00 5.65e-01 3.02e+02 angle pdb=" C ALA Z 188 " pdb=" CA ALA Z 188 " pdb=" CB ALA Z 188 " ideal model delta sigma weight residual 110.56 82.62 27.94 1.69e+00 3.50e-01 2.73e+02 ... (remaining 56274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.88: 23238 18.88 - 37.75: 1542 37.75 - 56.63: 344 56.63 - 75.51: 250 75.51 - 94.38: 127 Dihedral angle restraints: 25501 sinusoidal: 10350 harmonic: 15151 Sorted by residual: dihedral pdb=" CA HIS T 251 " pdb=" C HIS T 251 " pdb=" N GLU T 252 " pdb=" CA GLU T 252 " ideal model delta harmonic sigma weight residual -180.00 -85.62 -94.38 0 5.00e+00 4.00e-02 3.56e+02 dihedral pdb=" C ALA Z 188 " pdb=" N ALA Z 188 " pdb=" CA ALA Z 188 " pdb=" CB ALA Z 188 " ideal model delta harmonic sigma weight residual -122.60 -82.24 -40.36 0 2.50e+00 1.60e-01 2.61e+02 dihedral pdb=" CA SER T 91 " pdb=" C SER T 91 " pdb=" N ASN T 92 " pdb=" CA ASN T 92 " ideal model delta harmonic sigma weight residual 180.00 103.20 76.80 0 5.00e+00 4.00e-02 2.36e+02 ... (remaining 25498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 4644 0.196 - 0.393: 1522 0.393 - 0.589: 235 0.589 - 0.785: 37 0.785 - 0.981: 9 Chirality restraints: 6447 Sorted by residual: chirality pdb=" CA ASP S 375 " pdb=" N ASP S 375 " pdb=" C ASP S 375 " pdb=" CB ASP S 375 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CA ASN R 182 " pdb=" N ASN R 182 " pdb=" C ASN R 182 " pdb=" CB ASN R 182 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.90 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" CA ASP S 59 " pdb=" N ASP S 59 " pdb=" C ASP S 59 " pdb=" CB ASP S 59 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.96e+01 ... (remaining 6444 not shown) Planarity restraints: 7202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 99 " 0.366 2.00e-02 2.50e+03 2.97e-01 1.77e+03 pdb=" CG TYR R 99 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR R 99 " -0.307 2.00e-02 2.50e+03 pdb=" CD2 TYR R 99 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR R 99 " -0.392 2.00e-02 2.50e+03 pdb=" CE2 TYR R 99 " -0.070 2.00e-02 2.50e+03 pdb=" CZ TYR R 99 " -0.079 2.00e-02 2.50e+03 pdb=" OH TYR R 99 " 0.555 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 65 " 0.249 2.00e-02 2.50e+03 1.40e-01 3.90e+02 pdb=" CG TYR R 65 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR R 65 " -0.131 2.00e-02 2.50e+03 pdb=" CD2 TYR R 65 " -0.095 2.00e-02 2.50e+03 pdb=" CE1 TYR R 65 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR R 65 " -0.112 2.00e-02 2.50e+03 pdb=" CZ TYR R 65 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR R 65 " 0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Z 64 " -0.240 2.00e-02 2.50e+03 1.39e-01 3.86e+02 pdb=" CG TYR Z 64 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR Z 64 " 0.124 2.00e-02 2.50e+03 pdb=" CD2 TYR Z 64 " 0.115 2.00e-02 2.50e+03 pdb=" CE1 TYR Z 64 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 TYR Z 64 " 0.115 2.00e-02 2.50e+03 pdb=" CZ TYR Z 64 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR Z 64 " -0.216 2.00e-02 2.50e+03 ... (remaining 7199 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 7 1.91 - 2.65: 1033 2.65 - 3.40: 55880 3.40 - 4.15: 95668 4.15 - 4.90: 170141 Nonbonded interactions: 322729 Sorted by model distance: nonbonded pdb=" CE1 TYR O 33 " pdb=" CE2 PHE O 69 " model vdw 1.158 3.640 nonbonded pdb=" CE1 PHE O 69 " pdb=" CD LYS O 72 " model vdw 1.316 3.740 nonbonded pdb=" CD1 LEU O 14 " pdb=" CD1 LEU O 61 " model vdw 1.341 3.880 nonbonded pdb=" O ASP Y 33 " pdb=" N PHE Y 35 " model vdw 1.428 2.520 nonbonded pdb=" CE1 TYR O 33 " pdb=" CZ PHE O 69 " model vdw 1.507 3.640 ... (remaining 322724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.450 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 100.560 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4150 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.034 0.711 41662 Z= 2.198 Angle : 3.323 68.596 56279 Z= 2.303 Chirality : 0.190 0.981 6447 Planarity : 0.027 0.326 7202 Dihedral : 17.162 94.381 15677 Min Nonbonded Distance : 1.158 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 2.19 % Allowed : 5.23 % Favored : 92.58 % Rotamer: Outliers : 2.25 % Allowed : 5.79 % Favored : 91.95 % Cbeta Deviations : 6.05 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.10), residues: 5108 helix: -0.51 (0.08), residues: 3156 sheet: -1.01 (0.35), residues: 171 loop : -2.49 (0.12), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.190 0.041 TRP P 72 HIS 0.060 0.014 HIS U 252 PHE 0.166 0.037 PHE O 106 TYR 0.555 0.044 TYR R 99 ARG 0.109 0.010 ARG Z 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1728 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1625 time to evaluate : 4.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 72 ILE cc_start: 0.6797 (mm) cc_final: 0.6596 (mm) REVERT: W 105 VAL cc_start: 0.5855 (OUTLIER) cc_final: 0.5512 (t) REVERT: W 133 LYS cc_start: 0.5783 (pttm) cc_final: 0.5494 (pttm) REVERT: W 137 VAL cc_start: 0.7457 (t) cc_final: 0.7099 (t) REVERT: W 149 GLN cc_start: 0.3882 (OUTLIER) cc_final: 0.1995 (pp30) REVERT: V 34 LEU cc_start: 0.7533 (tp) cc_final: 0.7003 (tp) REVERT: V 173 THR cc_start: 0.6453 (p) cc_final: 0.5959 (p) REVERT: V 198 SER cc_start: 0.6879 (m) cc_final: 0.6639 (t) REVERT: V 215 ASN cc_start: 0.4967 (m-40) cc_final: 0.4646 (m-40) REVERT: V 235 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7078 (tm-30) REVERT: T 249 MET cc_start: 0.4303 (ptt) cc_final: 0.3861 (ptp) REVERT: T 265 ASP cc_start: 0.7101 (m-30) cc_final: 0.6531 (m-30) REVERT: X 14 VAL cc_start: 0.6507 (OUTLIER) cc_final: 0.6078 (m) REVERT: Z 138 ARG cc_start: 0.3611 (ptt180) cc_final: 0.1192 (tmt170) REVERT: Z 249 MET cc_start: 0.3745 (mmt) cc_final: 0.3174 (mmm) REVERT: Z 425 ILE cc_start: 0.4064 (mm) cc_final: 0.3399 (mm) REVERT: Z 595 MET cc_start: 0.4837 (mtm) cc_final: 0.4300 (mtm) REVERT: Z 793 PHE cc_start: 0.1024 (m-80) cc_final: 0.0808 (m-10) REVERT: N 294 PRO cc_start: 0.6033 (OUTLIER) cc_final: 0.3708 (Cg_endo) REVERT: N 428 VAL cc_start: 0.8132 (m) cc_final: 0.7764 (p) REVERT: N 485 MET cc_start: 0.6871 (mtm) cc_final: 0.6558 (mtm) REVERT: N 521 LEU cc_start: 0.6322 (mt) cc_final: 0.6010 (mt) REVERT: N 543 ASP cc_start: 0.7016 (t70) cc_final: 0.6803 (t70) REVERT: N 546 LEU cc_start: 0.7626 (mm) cc_final: 0.7293 (mm) REVERT: N 616 HIS cc_start: 0.6397 (m90) cc_final: 0.5965 (m90) REVERT: N 650 ASP cc_start: 0.5333 (m-30) cc_final: 0.4935 (t0) REVERT: N 683 LEU cc_start: 0.8293 (mt) cc_final: 0.8024 (mt) REVERT: N 742 TRP cc_start: 0.5359 (t-100) cc_final: 0.4651 (t-100) REVERT: S 456 ASP cc_start: 0.6631 (m-30) cc_final: 0.6281 (m-30) REVERT: S 465 ILE cc_start: 0.7560 (mt) cc_final: 0.6713 (mt) REVERT: P 16 ILE cc_start: 0.7230 (mt) cc_final: 0.6778 (mt) REVERT: P 224 LEU cc_start: 0.8334 (mt) cc_final: 0.7862 (mm) REVERT: P 308 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6437 (tp) REVERT: P 346 ILE cc_start: 0.6463 (mt) cc_final: 0.6022 (mt) REVERT: Q 52 ASN cc_start: 0.4291 (p0) cc_final: 0.3298 (t0) REVERT: Q 229 ASP cc_start: 0.6132 (m-30) cc_final: 0.5707 (t0) REVERT: Q 230 LYS cc_start: 0.6588 (mmtt) cc_final: 0.5759 (mmtm) REVERT: Q 234 THR cc_start: 0.6674 (p) cc_final: 0.5089 (p) REVERT: Q 381 ILE cc_start: 0.6467 (mt) cc_final: 0.6127 (mt) REVERT: Q 389 VAL cc_start: 0.6111 (m) cc_final: 0.5373 (m) REVERT: Q 434 TYR cc_start: 0.4966 (m-10) cc_final: 0.4187 (m-80) REVERT: R 333 MET cc_start: 0.7166 (mmm) cc_final: 0.6894 (mmm) REVERT: R 364 LEU cc_start: 0.6654 (tp) cc_final: 0.6266 (tp) REVERT: R 404 VAL cc_start: 0.7990 (m) cc_final: 0.7561 (p) REVERT: U 1 MET cc_start: 0.5211 (mtt) cc_final: 0.4964 (mtt) REVERT: U 15 LEU cc_start: 0.7838 (mt) cc_final: 0.7304 (mt) REVERT: U 17 SER cc_start: 0.7507 (m) cc_final: 0.6574 (t) REVERT: U 45 THR cc_start: 0.7439 (t) cc_final: 0.6929 (p) REVERT: U 65 VAL cc_start: 0.7731 (t) cc_final: 0.6341 (t) REVERT: U 73 ILE cc_start: 0.5669 (mt) cc_final: 0.5347 (mt) REVERT: U 116 ASN cc_start: 0.5949 (p0) cc_final: 0.5429 (p0) REVERT: U 171 VAL cc_start: 0.8436 (t) cc_final: 0.7478 (t) REVERT: U 229 LEU cc_start: 0.8005 (mt) cc_final: 0.7786 (mm) REVERT: U 247 ILE cc_start: 0.8559 (mt) cc_final: 0.8176 (mt) REVERT: O 112 LYS cc_start: 0.5789 (mttt) cc_final: 0.5564 (mttt) REVERT: O 173 SER cc_start: 0.5850 (t) cc_final: 0.4905 (p) REVERT: O 284 GLU cc_start: 0.4423 (tt0) cc_final: 0.3733 (tt0) outliers start: 103 outliers final: 18 residues processed: 1698 average time/residue: 0.5787 time to fit residues: 1566.9063 Evaluate side-chains 879 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 856 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 428 optimal weight: 6.9990 chunk 385 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 398 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 296 optimal weight: 5.9990 chunk 461 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 12 ASN W 80 GLN W 95 GLN ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 40 HIS V 73 GLN V 131 GLN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 195 HIS V 200 ASN V 222 GLN V 301 ASN T 112 ASN T 123 HIS T 132 HIS T 170 ASN T 230 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 17 GLN ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 168 GLN Z 235 GLN Z 247 GLN Z 332 ASN Z 347 ASN Z 361 HIS Z 387 ASN ** Z 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 769 ASN Z 771 HIS Z 917 ASN ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 931 GLN N 111 GLN ** N 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 306 ASN N 340 HIS ** N 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 ASN ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 525 ASN ** N 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 900 ASN S 20 HIS S 91 ASN S 112 ASN S 154 GLN S 159 ASN ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 191 HIS S 235 ASN S 243 ASN S 334 HIS ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 GLN P 306 ASN P 323 ASN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 342 GLN P 349 ASN P 413 ASN P 417 HIS ** P 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 GLN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 HIS Q 186 HIS Q 280 ASN ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 361 HIS Q 425 GLN R 35 GLN R 100 ASN R 132 GLN R 217 HIS R 397 ASN R 401 HIS R 415 GLN U 21 HIS ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 238 ASN U 251 ASN ** U 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 273 GLN O 283 HIS ** O 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4747 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 41662 Z= 0.310 Angle : 0.861 17.825 56279 Z= 0.462 Chirality : 0.046 0.455 6447 Planarity : 0.006 0.075 7202 Dihedral : 5.993 54.194 5504 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.37 % Favored : 95.16 % Rotamer: Outliers : 0.24 % Allowed : 4.79 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 5108 helix: 0.52 (0.09), residues: 3274 sheet: -1.06 (0.33), residues: 196 loop : -1.90 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP S 184 HIS 0.013 0.002 HIS P 230 PHE 0.036 0.003 PHE S 241 TYR 0.044 0.003 TYR V 197 ARG 0.010 0.001 ARG O 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1070 time to evaluate : 4.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 72 ILE cc_start: 0.6879 (mm) cc_final: 0.6632 (mm) REVERT: W 76 LEU cc_start: 0.7685 (tt) cc_final: 0.7448 (tt) REVERT: V 34 LEU cc_start: 0.7928 (tp) cc_final: 0.7483 (tp) REVERT: V 94 MET cc_start: 0.7097 (ppp) cc_final: 0.6461 (tmm) REVERT: V 116 CYS cc_start: 0.8799 (m) cc_final: 0.7986 (p) REVERT: T 249 MET cc_start: 0.5623 (ptt) cc_final: 0.5027 (ptp) REVERT: T 250 MET cc_start: 0.4517 (ptt) cc_final: 0.4145 (ptt) REVERT: X 74 MET cc_start: 0.6074 (tpp) cc_final: 0.5800 (tpt) REVERT: Z 249 MET cc_start: 0.4629 (mmt) cc_final: 0.4277 (mmt) REVERT: Z 405 ASN cc_start: 0.7686 (m110) cc_final: 0.7290 (m-40) REVERT: Z 525 MET cc_start: 0.5230 (ptp) cc_final: 0.4710 (ptt) REVERT: Z 592 GLU cc_start: 0.5630 (mm-30) cc_final: 0.5411 (mm-30) REVERT: Z 595 MET cc_start: 0.4755 (mtm) cc_final: 0.4445 (mtt) REVERT: Z 775 MET cc_start: 0.2825 (tmm) cc_final: 0.2503 (tmm) REVERT: Z 832 ARG cc_start: 0.4419 (mtm-85) cc_final: 0.3583 (ttm170) REVERT: N 329 HIS cc_start: 0.5895 (t-90) cc_final: 0.4646 (t-90) REVERT: N 338 PHE cc_start: 0.6405 (m-80) cc_final: 0.6133 (m-80) REVERT: N 428 VAL cc_start: 0.8118 (m) cc_final: 0.7888 (p) REVERT: N 448 LEU cc_start: 0.7513 (mt) cc_final: 0.7139 (mt) REVERT: N 450 ILE cc_start: 0.8021 (tt) cc_final: 0.7732 (tt) REVERT: N 581 ASP cc_start: 0.6053 (m-30) cc_final: 0.5793 (m-30) REVERT: N 583 VAL cc_start: 0.8615 (t) cc_final: 0.8212 (t) REVERT: N 595 LEU cc_start: 0.7012 (mp) cc_final: 0.6356 (mt) REVERT: N 616 HIS cc_start: 0.6705 (m90) cc_final: 0.6238 (m90) REVERT: N 678 ILE cc_start: 0.8241 (mt) cc_final: 0.7888 (mt) REVERT: S 232 MET cc_start: 0.5903 (mmp) cc_final: 0.4843 (mmp) REVERT: S 422 MET cc_start: 0.7515 (mmp) cc_final: 0.7222 (mmm) REVERT: P 281 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.6830 (mp) REVERT: P 412 LEU cc_start: 0.8674 (mt) cc_final: 0.8417 (mt) REVERT: Q 124 PHE cc_start: 0.4924 (m-80) cc_final: 0.4398 (m-80) REVERT: Q 234 THR cc_start: 0.6253 (p) cc_final: 0.4839 (p) REVERT: R 333 MET cc_start: 0.6691 (mmm) cc_final: 0.6431 (mmm) REVERT: R 337 VAL cc_start: 0.7474 (m) cc_final: 0.7158 (p) REVERT: R 405 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7598 (mmtt) REVERT: U 13 LEU cc_start: 0.8461 (tp) cc_final: 0.8251 (tt) REVERT: U 14 VAL cc_start: 0.8244 (t) cc_final: 0.8011 (t) REVERT: U 17 SER cc_start: 0.8088 (m) cc_final: 0.7039 (t) REVERT: U 104 LEU cc_start: 0.7431 (mt) cc_final: 0.5606 (mt) REVERT: U 226 LEU cc_start: 0.7093 (mt) cc_final: 0.6828 (mt) REVERT: O 12 SER cc_start: 0.8903 (m) cc_final: 0.8533 (p) REVERT: O 223 LEU cc_start: 0.6025 (mt) cc_final: 0.5752 (mt) REVERT: O 352 TRP cc_start: 0.4747 (t60) cc_final: 0.4456 (t60) outliers start: 11 outliers final: 1 residues processed: 1078 average time/residue: 0.5057 time to fit residues: 892.8030 Evaluate side-chains 741 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 739 time to evaluate : 4.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 256 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 383 optimal weight: 9.9990 chunk 314 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 462 optimal weight: 10.0000 chunk 499 optimal weight: 7.9990 chunk 411 optimal weight: 4.9990 chunk 458 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 370 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 12 ASN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 279 HIS T 92 ASN T 94 HIS T 230 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 ASN ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 247 GLN Z 361 HIS ** Z 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 622 HIS Z 856 HIS Z 899 GLN ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 ASN N 256 GLN N 268 GLN N 300 ASN ** N 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 512 ASN N 580 ASN N 654 GLN N 707 ASN ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 900 ASN ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 417 GLN P 38 GLN ** P 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 GLN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS P 386 GLN P 418 ASN ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN Q 248 ASN ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 405 GLN R 340 GLN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 252 HIS U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 177 GLN O 282 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5013 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 41662 Z= 0.297 Angle : 0.782 16.464 56279 Z= 0.417 Chirality : 0.043 0.216 6447 Planarity : 0.005 0.066 7202 Dihedral : 5.785 40.711 5504 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.93 % Favored : 94.71 % Rotamer: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5108 helix: 0.31 (0.09), residues: 3315 sheet: -1.22 (0.32), residues: 219 loop : -1.84 (0.14), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.003 TRP T 226 HIS 0.016 0.002 HIS U 21 PHE 0.031 0.003 PHE N 697 TYR 0.044 0.003 TYR V 197 ARG 0.019 0.001 ARG T 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 987 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.2321 (ttt) cc_final: 0.1544 (ttm) REVERT: V 34 LEU cc_start: 0.8088 (tp) cc_final: 0.7298 (tp) REVERT: V 126 GLN cc_start: 0.7587 (mm110) cc_final: 0.7234 (tp40) REVERT: V 173 THR cc_start: 0.6938 (m) cc_final: 0.6486 (m) REVERT: T 62 LEU cc_start: 0.6645 (mt) cc_final: 0.6402 (mt) REVERT: T 144 TYR cc_start: 0.3655 (t80) cc_final: 0.2846 (m-80) REVERT: T 249 MET cc_start: 0.6102 (ptt) cc_final: 0.5031 (ptp) REVERT: X 125 MET cc_start: 0.6453 (tmm) cc_final: 0.6056 (tmm) REVERT: Z 121 ILE cc_start: 0.5919 (pt) cc_final: 0.5559 (pt) REVERT: Z 243 GLN cc_start: 0.6164 (pp30) cc_final: 0.5600 (pp30) REVERT: Z 247 GLN cc_start: 0.3353 (OUTLIER) cc_final: 0.2922 (pp30) REVERT: Z 249 MET cc_start: 0.5102 (mmt) cc_final: 0.4871 (mmt) REVERT: Z 406 TRP cc_start: 0.5916 (p-90) cc_final: 0.5334 (t-100) REVERT: Z 525 MET cc_start: 0.4574 (ptp) cc_final: 0.4267 (ptp) REVERT: Z 595 MET cc_start: 0.5295 (mtm) cc_final: 0.4785 (mtt) REVERT: Z 775 MET cc_start: 0.2191 (tmm) cc_final: 0.1795 (tmm) REVERT: Z 832 ARG cc_start: 0.3893 (mtm-85) cc_final: 0.3563 (ttm170) REVERT: N 428 VAL cc_start: 0.8451 (m) cc_final: 0.8172 (p) REVERT: N 448 LEU cc_start: 0.7592 (mt) cc_final: 0.6615 (mt) REVERT: N 450 ILE cc_start: 0.7855 (tt) cc_final: 0.7427 (tt) REVERT: N 457 SER cc_start: 0.8715 (p) cc_final: 0.8493 (t) REVERT: N 521 LEU cc_start: 0.8646 (mt) cc_final: 0.8285 (mt) REVERT: N 543 ASP cc_start: 0.6539 (t70) cc_final: 0.6149 (t70) REVERT: N 548 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7895 (mmt90) REVERT: N 581 ASP cc_start: 0.6147 (m-30) cc_final: 0.5868 (m-30) REVERT: N 595 LEU cc_start: 0.6883 (mp) cc_final: 0.6544 (mt) REVERT: N 616 HIS cc_start: 0.6986 (m90) cc_final: 0.6228 (m90) REVERT: N 652 VAL cc_start: 0.8218 (t) cc_final: 0.7939 (t) REVERT: N 678 ILE cc_start: 0.8551 (mt) cc_final: 0.7549 (mm) REVERT: S 232 MET cc_start: 0.6161 (mmp) cc_final: 0.5422 (mmp) REVERT: P 19 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6392 (pp20) REVERT: P 96 MET cc_start: 0.6342 (mmp) cc_final: 0.5898 (mmp) REVERT: P 194 SER cc_start: 0.7255 (t) cc_final: 0.6979 (t) REVERT: P 281 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7761 (mt) REVERT: P 362 LEU cc_start: 0.6818 (mt) cc_final: 0.6503 (mt) REVERT: Q 351 ILE cc_start: 0.7562 (pt) cc_final: 0.7194 (pt) REVERT: Q 385 ILE cc_start: 0.8679 (pt) cc_final: 0.8374 (pt) REVERT: R 333 MET cc_start: 0.6761 (mmm) cc_final: 0.6412 (mmm) REVERT: U 1 MET cc_start: 0.5163 (mtm) cc_final: 0.4941 (mtm) REVERT: U 17 SER cc_start: 0.7871 (m) cc_final: 0.7474 (t) REVERT: U 194 LEU cc_start: 0.6254 (tp) cc_final: 0.5860 (tp) REVERT: U 226 LEU cc_start: 0.7457 (mt) cc_final: 0.6967 (mt) REVERT: U 229 LEU cc_start: 0.8230 (mm) cc_final: 0.7932 (mm) REVERT: U 235 LEU cc_start: 0.8052 (mp) cc_final: 0.7808 (mt) REVERT: U 261 LEU cc_start: 0.7450 (mp) cc_final: 0.7247 (mp) REVERT: O 12 SER cc_start: 0.8746 (m) cc_final: 0.8504 (p) outliers start: 8 outliers final: 3 residues processed: 993 average time/residue: 0.5171 time to fit residues: 837.1126 Evaluate side-chains 730 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 724 time to evaluate : 4.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 456 optimal weight: 8.9990 chunk 347 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 220 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 463 optimal weight: 8.9990 chunk 491 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 439 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 29 GLN V 88 GLN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 279 HIS ** V 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 237 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 842 GLN ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN N 268 GLN ** N 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 375 HIS ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 616 HIS ** N 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 870 ASN ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 GLN S 91 ASN S 154 GLN ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 205 ASN ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 263 HIS ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 GLN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 418 ASN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 340 GLN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 230 GLN U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 283 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 41662 Z= 0.244 Angle : 0.706 16.499 56279 Z= 0.373 Chirality : 0.042 0.436 6447 Planarity : 0.005 0.072 7202 Dihedral : 5.521 37.093 5504 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.46 % Favored : 95.16 % Rotamer: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 5108 helix: 0.54 (0.09), residues: 3321 sheet: -1.13 (0.32), residues: 212 loop : -1.73 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP T 226 HIS 0.011 0.001 HIS U 21 PHE 0.037 0.002 PHE Q 335 TYR 0.039 0.002 TYR Z 738 ARG 0.007 0.001 ARG N 548 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 953 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.2414 (ttt) cc_final: 0.1488 (ttm) REVERT: W 141 ILE cc_start: 0.4315 (pt) cc_final: 0.3792 (mp) REVERT: V 34 LEU cc_start: 0.8364 (tp) cc_final: 0.8003 (tp) REVERT: V 95 LEU cc_start: 0.7204 (mt) cc_final: 0.6960 (mt) REVERT: V 96 LYS cc_start: 0.7205 (mttt) cc_final: 0.6884 (mttt) REVERT: V 173 THR cc_start: 0.7749 (m) cc_final: 0.7307 (m) REVERT: V 251 TYR cc_start: 0.7207 (t80) cc_final: 0.6994 (t80) REVERT: V 280 LEU cc_start: 0.8683 (mt) cc_final: 0.8307 (mt) REVERT: T 144 TYR cc_start: 0.3973 (t80) cc_final: 0.2840 (m-80) REVERT: T 249 MET cc_start: 0.5898 (ptt) cc_final: 0.5086 (ptp) REVERT: X 125 MET cc_start: 0.6571 (tmm) cc_final: 0.6370 (tmm) REVERT: Z 153 TYR cc_start: 0.1230 (p90) cc_final: -0.0402 (p90) REVERT: Z 249 MET cc_start: 0.4821 (mmt) cc_final: 0.4506 (mmt) REVERT: Z 406 TRP cc_start: 0.5891 (p-90) cc_final: 0.5120 (t-100) REVERT: Z 525 MET cc_start: 0.4638 (ptp) cc_final: 0.4296 (ptp) REVERT: Z 595 MET cc_start: 0.5370 (mtm) cc_final: 0.4924 (mtt) REVERT: Z 832 ARG cc_start: 0.3750 (mtm-85) cc_final: 0.3516 (ttm110) REVERT: N 166 ILE cc_start: 0.4941 (mm) cc_final: 0.4689 (mm) REVERT: N 217 MET cc_start: 0.4157 (mmp) cc_final: 0.3909 (mmp) REVERT: N 271 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6639 (mm-30) REVERT: N 428 VAL cc_start: 0.8498 (m) cc_final: 0.8101 (p) REVERT: N 448 LEU cc_start: 0.7663 (mt) cc_final: 0.6631 (mt) REVERT: N 450 ILE cc_start: 0.8019 (tt) cc_final: 0.7657 (tt) REVERT: N 457 SER cc_start: 0.8885 (p) cc_final: 0.8593 (t) REVERT: N 595 LEU cc_start: 0.6964 (mp) cc_final: 0.6642 (mt) REVERT: N 678 ILE cc_start: 0.8088 (mt) cc_final: 0.7323 (mm) REVERT: N 782 PHE cc_start: 0.4260 (m-80) cc_final: 0.4040 (m-10) REVERT: S 211 ARG cc_start: 0.5601 (tmm160) cc_final: 0.5212 (ttp80) REVERT: S 232 MET cc_start: 0.5845 (mmp) cc_final: 0.5269 (mmp) REVERT: S 477 VAL cc_start: 0.8408 (m) cc_final: 0.7808 (m) REVERT: P 362 LEU cc_start: 0.7183 (mt) cc_final: 0.6644 (mt) REVERT: Q 281 ILE cc_start: 0.7857 (mt) cc_final: 0.7519 (mt) REVERT: R 171 MET cc_start: 0.5783 (ttp) cc_final: 0.4778 (tmm) REVERT: R 172 LEU cc_start: 0.7653 (mt) cc_final: 0.7315 (mt) REVERT: R 209 ARG cc_start: 0.7529 (mtm180) cc_final: 0.6857 (mtp180) REVERT: R 243 LEU cc_start: 0.6859 (mt) cc_final: 0.6624 (mt) REVERT: R 333 MET cc_start: 0.6920 (mmm) cc_final: 0.6625 (mmm) REVERT: U 14 VAL cc_start: 0.7956 (t) cc_final: 0.7520 (t) REVERT: U 17 SER cc_start: 0.8170 (m) cc_final: 0.7856 (t) REVERT: U 194 LEU cc_start: 0.6338 (tp) cc_final: 0.6042 (tp) REVERT: U 247 ILE cc_start: 0.8641 (tp) cc_final: 0.8359 (tp) REVERT: O 143 LEU cc_start: 0.7390 (mt) cc_final: 0.6874 (mt) REVERT: O 194 LEU cc_start: 0.7336 (mm) cc_final: 0.7002 (mm) REVERT: O 373 TRP cc_start: 0.5912 (t60) cc_final: 0.5698 (t60) outliers start: 4 outliers final: 0 residues processed: 956 average time/residue: 0.5173 time to fit residues: 808.8631 Evaluate side-chains 726 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 726 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 408 optimal weight: 0.0040 chunk 278 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 365 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 419 optimal weight: 8.9990 chunk 339 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 250 optimal weight: 10.0000 chunk 440 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 12 ASN W 29 GLN W 100 HIS ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 215 ASN T 92 ASN ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 204 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 151 HIS ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 580 GLN ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 ASN N 233 ASN N 256 GLN N 268 GLN ** N 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 375 HIS ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 205 ASN ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 425 GLN ** R 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 ASN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 230 GLN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 294 ASN O 117 ASN ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN O 235 HIS O 282 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 0.8021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 41662 Z= 0.257 Angle : 0.715 19.154 56279 Z= 0.378 Chirality : 0.042 0.309 6447 Planarity : 0.005 0.067 7202 Dihedral : 5.512 40.242 5504 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.13 % Favored : 94.48 % Rotamer: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 5108 helix: 0.43 (0.09), residues: 3333 sheet: -1.17 (0.32), residues: 219 loop : -1.67 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP T 226 HIS 0.015 0.002 HIS O 235 PHE 0.033 0.002 PHE N 682 TYR 0.033 0.002 TYR O 172 ARG 0.006 0.001 ARG S 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 897 time to evaluate : 5.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 29 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7050 (mm-40) REVERT: W 85 LEU cc_start: 0.7432 (tp) cc_final: 0.7154 (tp) REVERT: W 173 THR cc_start: 0.6845 (m) cc_final: 0.6499 (m) REVERT: V 34 LEU cc_start: 0.8482 (tp) cc_final: 0.8161 (tp) REVERT: V 57 PHE cc_start: 0.6427 (t80) cc_final: 0.6132 (t80) REVERT: V 116 CYS cc_start: 0.8955 (m) cc_final: 0.8721 (m) REVERT: T 116 GLN cc_start: 0.5346 (pt0) cc_final: 0.5078 (pt0) REVERT: T 249 MET cc_start: 0.5666 (ptt) cc_final: 0.4959 (ptp) REVERT: X 74 MET cc_start: 0.5866 (tpp) cc_final: 0.5439 (tpt) REVERT: X 125 MET cc_start: 0.6580 (tmm) cc_final: 0.6329 (tmm) REVERT: Y 65 ASP cc_start: 0.3168 (p0) cc_final: 0.2915 (p0) REVERT: Z 153 TYR cc_start: 0.0834 (p90) cc_final: -0.1294 (p90) REVERT: Z 249 MET cc_start: 0.4944 (mmt) cc_final: 0.4655 (mmt) REVERT: Z 406 TRP cc_start: 0.5798 (p-90) cc_final: 0.5376 (t-100) REVERT: Z 455 ILE cc_start: 0.3694 (mm) cc_final: 0.3438 (tp) REVERT: Z 525 MET cc_start: 0.4722 (ptp) cc_final: 0.4308 (ptp) REVERT: Z 595 MET cc_start: 0.5374 (mtm) cc_final: 0.4926 (mtt) REVERT: N 166 ILE cc_start: 0.5083 (mm) cc_final: 0.4860 (mm) REVERT: N 448 LEU cc_start: 0.7588 (mt) cc_final: 0.6608 (mt) REVERT: N 450 ILE cc_start: 0.8098 (tt) cc_final: 0.7743 (tt) REVERT: N 457 SER cc_start: 0.8761 (p) cc_final: 0.8504 (t) REVERT: S 58 LYS cc_start: 0.5195 (mtmt) cc_final: 0.3952 (ttmt) REVERT: S 232 MET cc_start: 0.5891 (mmp) cc_final: 0.5595 (mmp) REVERT: S 477 VAL cc_start: 0.8662 (m) cc_final: 0.7773 (m) REVERT: P 362 LEU cc_start: 0.6996 (mt) cc_final: 0.6724 (mt) REVERT: P 364 ARG cc_start: 0.5603 (mpt180) cc_final: 0.5014 (mtm-85) REVERT: P 380 ILE cc_start: 0.7613 (pt) cc_final: 0.7256 (mt) REVERT: Q 98 LYS cc_start: 0.7546 (tptp) cc_final: 0.6988 (tptp) REVERT: Q 416 VAL cc_start: 0.7600 (t) cc_final: 0.7218 (t) REVERT: R 171 MET cc_start: 0.5727 (ttp) cc_final: 0.5265 (tmm) REVERT: R 172 LEU cc_start: 0.7736 (mt) cc_final: 0.7254 (mt) REVERT: R 333 MET cc_start: 0.6964 (mmm) cc_final: 0.6595 (mmm) REVERT: U 17 SER cc_start: 0.8385 (m) cc_final: 0.7911 (t) REVERT: U 194 LEU cc_start: 0.6547 (tp) cc_final: 0.5897 (tp) REVERT: U 229 LEU cc_start: 0.8007 (mm) cc_final: 0.7765 (mm) REVERT: U 247 ILE cc_start: 0.8598 (tp) cc_final: 0.8321 (tp) REVERT: U 274 MET cc_start: 0.7422 (ttt) cc_final: 0.7184 (ttt) REVERT: O 143 LEU cc_start: 0.7489 (mt) cc_final: 0.7277 (mt) REVERT: O 223 LEU cc_start: 0.5928 (mt) cc_final: 0.5411 (mt) outliers start: 3 outliers final: 1 residues processed: 900 average time/residue: 0.5394 time to fit residues: 799.9253 Evaluate side-chains 713 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 711 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 165 optimal weight: 20.0000 chunk 442 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 491 optimal weight: 10.0000 chunk 408 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 29 GLN W 58 ASN W 150 ASN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 217 HIS ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 204 ASN ** T 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 GLN N 233 ASN N 256 GLN N 268 GLN ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 900 ASN S 143 GLN S 159 ASN ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 205 ASN ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 183 GLN ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 ASN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 HIS ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 366 ASN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 216 ASN U 230 GLN U 256 ASN ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN O 343 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5238 moved from start: 0.8628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41662 Z= 0.270 Angle : 0.735 16.398 56279 Z= 0.387 Chirality : 0.043 0.259 6447 Planarity : 0.005 0.067 7202 Dihedral : 5.592 43.876 5504 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.09 % Favored : 94.52 % Rotamer: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5108 helix: 0.26 (0.09), residues: 3326 sheet: -1.07 (0.31), residues: 221 loop : -1.75 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP T 226 HIS 0.010 0.002 HIS V 40 PHE 0.033 0.002 PHE N 682 TYR 0.028 0.002 TYR N 298 ARG 0.013 0.001 ARG V 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 900 time to evaluate : 4.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 85 LEU cc_start: 0.7479 (tp) cc_final: 0.7202 (tp) REVERT: W 137 VAL cc_start: 0.6825 (t) cc_final: 0.6618 (t) REVERT: W 167 GLU cc_start: 0.4848 (tt0) cc_final: 0.4278 (tt0) REVERT: V 34 LEU cc_start: 0.8486 (tp) cc_final: 0.8059 (tp) REVERT: V 57 PHE cc_start: 0.6586 (t80) cc_final: 0.6332 (t80) REVERT: V 73 GLN cc_start: 0.8083 (pp30) cc_final: 0.7829 (pp30) REVERT: V 116 CYS cc_start: 0.8822 (m) cc_final: 0.8560 (m) REVERT: V 233 LYS cc_start: 0.7854 (mttt) cc_final: 0.7115 (mttt) REVERT: V 279 HIS cc_start: 0.5705 (m-70) cc_final: 0.5429 (m-70) REVERT: V 280 LEU cc_start: 0.8687 (mt) cc_final: 0.8441 (mt) REVERT: T 110 LEU cc_start: 0.6940 (mt) cc_final: 0.6662 (mt) REVERT: X 125 MET cc_start: 0.6565 (tmm) cc_final: 0.6297 (tmm) REVERT: Y 65 ASP cc_start: 0.2819 (p0) cc_final: 0.2531 (p0) REVERT: Z 249 MET cc_start: 0.4545 (mmt) cc_final: 0.4126 (mmm) REVERT: Z 406 TRP cc_start: 0.5805 (p-90) cc_final: 0.5212 (t-100) REVERT: Z 525 MET cc_start: 0.5103 (ptp) cc_final: 0.4669 (ptp) REVERT: Z 595 MET cc_start: 0.5415 (mtm) cc_final: 0.4951 (mtt) REVERT: Z 793 PHE cc_start: -0.0262 (m-10) cc_final: -0.0717 (m-10) REVERT: N 166 ILE cc_start: 0.5286 (mm) cc_final: 0.5069 (mm) REVERT: N 301 THR cc_start: 0.6237 (m) cc_final: 0.5858 (m) REVERT: N 457 SER cc_start: 0.8915 (p) cc_final: 0.8606 (t) REVERT: N 512 ASN cc_start: 0.8019 (p0) cc_final: 0.7092 (p0) REVERT: N 521 LEU cc_start: 0.8716 (mt) cc_final: 0.8415 (mt) REVERT: N 525 ASN cc_start: 0.8442 (m-40) cc_final: 0.8011 (m-40) REVERT: N 572 LEU cc_start: 0.8264 (pp) cc_final: 0.7564 (tp) REVERT: S 58 LYS cc_start: 0.5147 (mtmt) cc_final: 0.3605 (ttmt) REVERT: S 232 MET cc_start: 0.6196 (mmp) cc_final: 0.5848 (mmp) REVERT: S 421 TYR cc_start: 0.6862 (m-80) cc_final: 0.6542 (m-80) REVERT: P 171 MET cc_start: 0.3899 (ppp) cc_final: 0.3562 (mtp) REVERT: P 341 LEU cc_start: 0.7602 (mt) cc_final: 0.7351 (mt) REVERT: P 364 ARG cc_start: 0.5743 (mpt180) cc_final: 0.5316 (mtm-85) REVERT: Q 63 GLN cc_start: 0.6617 (tp40) cc_final: 0.6381 (mm-40) REVERT: Q 98 LYS cc_start: 0.7797 (tptp) cc_final: 0.7595 (tptp) REVERT: Q 99 THR cc_start: 0.7054 (p) cc_final: 0.6741 (p) REVERT: Q 210 CYS cc_start: 0.5559 (m) cc_final: 0.5135 (m) REVERT: Q 416 VAL cc_start: 0.7703 (t) cc_final: 0.7363 (t) REVERT: Q 420 ASN cc_start: 0.6344 (m-40) cc_final: 0.5797 (m-40) REVERT: Q 434 TYR cc_start: 0.6349 (m-80) cc_final: 0.5853 (m-80) REVERT: R 171 MET cc_start: 0.5397 (ttp) cc_final: 0.4832 (tmm) REVERT: R 172 LEU cc_start: 0.7591 (mt) cc_final: 0.7075 (mt) REVERT: R 192 GLU cc_start: 0.6211 (mm-30) cc_final: 0.5574 (mm-30) REVERT: R 197 MET cc_start: 0.4882 (ptp) cc_final: 0.3954 (ptp) REVERT: U 14 VAL cc_start: 0.7965 (t) cc_final: 0.7571 (t) REVERT: U 17 SER cc_start: 0.8495 (m) cc_final: 0.8182 (t) REVERT: U 247 ILE cc_start: 0.8617 (tp) cc_final: 0.8388 (tp) REVERT: U 261 LEU cc_start: 0.7594 (mp) cc_final: 0.7248 (mp) REVERT: U 274 MET cc_start: 0.7603 (ttt) cc_final: 0.7283 (ttt) REVERT: O 85 SER cc_start: 0.7837 (m) cc_final: 0.7292 (p) outliers start: 4 outliers final: 1 residues processed: 903 average time/residue: 0.5184 time to fit residues: 764.1873 Evaluate side-chains 698 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 697 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 473 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 280 optimal weight: 0.9990 chunk 358 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 274 optimal weight: 8.9990 chunk 489 optimal weight: 20.0000 chunk 306 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 42 ASN W 86 HIS ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 220 GLN ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 539 ASN Z 549 ASN ** Z 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 593 HIS Z 766 HIS Z 842 GLN ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN N 375 HIS ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 667 GLN N 738 GLN N 900 ASN ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 312 GLN ** S 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 278 ASN ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN Q 361 HIS ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 256 ASN U 260 ASN ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN O 343 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5226 moved from start: 0.8903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 41662 Z= 0.236 Angle : 0.700 15.307 56279 Z= 0.370 Chirality : 0.042 0.277 6447 Planarity : 0.005 0.075 7202 Dihedral : 5.460 42.412 5504 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.19 % Favored : 94.42 % Rotamer: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.11), residues: 5108 helix: 0.32 (0.09), residues: 3350 sheet: -0.89 (0.32), residues: 223 loop : -1.71 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 54 HIS 0.007 0.001 HIS O 235 PHE 0.040 0.002 PHE O 65 TYR 0.032 0.002 TYR Z 738 ARG 0.013 0.001 ARG Q 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 910 time to evaluate : 4.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 137 VAL cc_start: 0.6685 (t) cc_final: 0.6462 (t) REVERT: W 167 GLU cc_start: 0.4774 (tt0) cc_final: 0.4307 (tt0) REVERT: V 157 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6404 (tpp80) REVERT: V 233 LYS cc_start: 0.7381 (mttt) cc_final: 0.6881 (mttt) REVERT: V 279 HIS cc_start: 0.5690 (m-70) cc_final: 0.5467 (m-70) REVERT: T 116 GLN cc_start: 0.5408 (pt0) cc_final: 0.4933 (pt0) REVERT: T 249 MET cc_start: 0.5087 (ptt) cc_final: 0.4668 (ptp) REVERT: X 74 MET cc_start: 0.4801 (tpt) cc_final: 0.4454 (tpt) REVERT: X 125 MET cc_start: 0.6617 (tmm) cc_final: 0.6337 (tmm) REVERT: Z 153 TYR cc_start: 0.1361 (p90) cc_final: -0.0970 (p90) REVERT: Z 249 MET cc_start: 0.4226 (mmt) cc_final: 0.3881 (mmm) REVERT: Z 525 MET cc_start: 0.5116 (ptp) cc_final: 0.4609 (ptp) REVERT: Z 595 MET cc_start: 0.4948 (mtm) cc_final: 0.4271 (mtt) REVERT: Z 756 MET cc_start: 0.5554 (mmt) cc_final: 0.5295 (mmt) REVERT: Z 793 PHE cc_start: -0.0154 (m-10) cc_final: -0.0529 (m-10) REVERT: N 166 ILE cc_start: 0.5352 (mm) cc_final: 0.4975 (mm) REVERT: N 301 THR cc_start: 0.6320 (m) cc_final: 0.5755 (m) REVERT: N 450 ILE cc_start: 0.7877 (tp) cc_final: 0.7158 (tt) REVERT: N 457 SER cc_start: 0.8936 (p) cc_final: 0.8657 (t) REVERT: N 519 VAL cc_start: 0.7977 (t) cc_final: 0.7693 (t) REVERT: N 521 LEU cc_start: 0.8725 (mt) cc_final: 0.8404 (mt) REVERT: N 525 ASN cc_start: 0.8370 (m-40) cc_final: 0.7949 (m-40) REVERT: N 572 LEU cc_start: 0.8195 (pp) cc_final: 0.7537 (tp) REVERT: N 582 ASP cc_start: 0.7288 (p0) cc_final: 0.7020 (p0) REVERT: S 58 LYS cc_start: 0.4869 (mtmt) cc_final: 0.3247 (ttmt) REVERT: S 232 MET cc_start: 0.6013 (mmp) cc_final: 0.5677 (mmp) REVERT: S 240 ASP cc_start: 0.5935 (t0) cc_final: 0.5599 (t0) REVERT: S 257 LEU cc_start: 0.7575 (tp) cc_final: 0.7281 (tp) REVERT: S 273 PHE cc_start: 0.7298 (m-80) cc_final: 0.7058 (m-80) REVERT: S 421 TYR cc_start: 0.6963 (m-80) cc_final: 0.6208 (m-80) REVERT: P 341 LEU cc_start: 0.7515 (mt) cc_final: 0.7249 (mt) REVERT: P 362 LEU cc_start: 0.6371 (mt) cc_final: 0.6046 (mt) REVERT: P 364 ARG cc_start: 0.6241 (mpt180) cc_final: 0.5969 (mtm-85) REVERT: P 412 LEU cc_start: 0.7769 (mt) cc_final: 0.7523 (mt) REVERT: Q 63 GLN cc_start: 0.6569 (tp40) cc_final: 0.6344 (mm-40) REVERT: Q 98 LYS cc_start: 0.7789 (tptp) cc_final: 0.7270 (tptp) REVERT: Q 210 CYS cc_start: 0.4809 (m) cc_final: 0.4302 (m) REVERT: Q 416 VAL cc_start: 0.7638 (t) cc_final: 0.7321 (t) REVERT: Q 420 ASN cc_start: 0.6278 (m-40) cc_final: 0.5879 (m-40) REVERT: Q 434 TYR cc_start: 0.6774 (m-10) cc_final: 0.6241 (m-80) REVERT: R 197 MET cc_start: 0.4735 (ptp) cc_final: 0.3875 (ptp) REVERT: R 353 MET cc_start: 0.3881 (pmm) cc_final: 0.2887 (pmm) REVERT: U 17 SER cc_start: 0.8516 (m) cc_final: 0.8067 (t) REVERT: U 104 LEU cc_start: 0.7377 (mt) cc_final: 0.7091 (mt) REVERT: U 229 LEU cc_start: 0.7939 (mm) cc_final: 0.7657 (mm) REVERT: U 247 ILE cc_start: 0.8687 (tp) cc_final: 0.8390 (tp) REVERT: U 261 LEU cc_start: 0.7683 (mp) cc_final: 0.7318 (mp) REVERT: U 274 MET cc_start: 0.7752 (ttt) cc_final: 0.7386 (ttt) REVERT: O 32 PHE cc_start: 0.7250 (m-10) cc_final: 0.6786 (m-10) REVERT: O 350 ILE cc_start: 0.8588 (mm) cc_final: 0.8368 (pt) outliers start: 2 outliers final: 0 residues processed: 911 average time/residue: 0.5118 time to fit residues: 764.4678 Evaluate side-chains 697 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 697 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 302 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 chunk 292 optimal weight: 4.9990 chunk 147 optimal weight: 30.0000 chunk 96 optimal weight: 0.0170 chunk 94 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 384 optimal weight: 1.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 88 GLN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 204 ASN ** Y 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 ASN Z 215 ASN Z 275 GLN Z 317 GLN Z 361 HIS Z 539 ASN Z 577 GLN ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 900 ASN ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 315 GLN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 407 ASN ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN Q 361 HIS ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 ASN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 256 ASN ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN O 343 GLN O 389 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5167 moved from start: 0.9096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41662 Z= 0.195 Angle : 0.674 14.287 56279 Z= 0.354 Chirality : 0.041 0.242 6447 Planarity : 0.004 0.065 7202 Dihedral : 5.273 38.446 5504 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.84 % Favored : 94.81 % Rotamer: Outliers : 0.04 % Allowed : 1.27 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 5108 helix: 0.44 (0.09), residues: 3366 sheet: -0.76 (0.33), residues: 216 loop : -1.71 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP T 151 HIS 0.007 0.001 HIS O 235 PHE 0.039 0.002 PHE N 682 TYR 0.033 0.002 TYR R 140 ARG 0.007 0.001 ARG R 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 914 time to evaluate : 4.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.1420 (ttt) cc_final: 0.1133 (ttt) REVERT: W 137 VAL cc_start: 0.6722 (t) cc_final: 0.6362 (t) REVERT: W 153 LEU cc_start: 0.7790 (mm) cc_final: 0.6778 (mm) REVERT: W 167 GLU cc_start: 0.4633 (tt0) cc_final: 0.4424 (tt0) REVERT: V 73 GLN cc_start: 0.8026 (pp30) cc_final: 0.7765 (pp30) REVERT: V 95 LEU cc_start: 0.7190 (mt) cc_final: 0.6782 (mt) REVERT: V 116 CYS cc_start: 0.8786 (m) cc_final: 0.8502 (m) REVERT: V 285 ASP cc_start: 0.5582 (t70) cc_final: 0.5175 (t0) REVERT: V 289 GLU cc_start: 0.5689 (pt0) cc_final: 0.5025 (pt0) REVERT: T 249 MET cc_start: 0.4988 (ptt) cc_final: 0.4658 (ptp) REVERT: X 74 MET cc_start: 0.4417 (tpt) cc_final: 0.3844 (tpp) REVERT: X 125 MET cc_start: 0.6753 (tmm) cc_final: 0.6380 (tmm) REVERT: Z 9 GLN cc_start: 0.2044 (mm110) cc_final: 0.1044 (tp-100) REVERT: Z 153 TYR cc_start: 0.1381 (p90) cc_final: -0.1142 (p90) REVERT: Z 525 MET cc_start: 0.5345 (ptp) cc_final: 0.4882 (ptp) REVERT: Z 595 MET cc_start: 0.4910 (mtm) cc_final: 0.4248 (mtt) REVERT: Z 756 MET cc_start: 0.5444 (mmt) cc_final: 0.5190 (mmt) REVERT: Z 793 PHE cc_start: -0.0330 (m-10) cc_final: -0.0684 (m-10) REVERT: N 301 THR cc_start: 0.6581 (m) cc_final: 0.6016 (m) REVERT: N 338 PHE cc_start: 0.6776 (m-80) cc_final: 0.6548 (m-80) REVERT: N 450 ILE cc_start: 0.7684 (tp) cc_final: 0.7069 (tt) REVERT: N 457 SER cc_start: 0.8937 (p) cc_final: 0.8641 (t) REVERT: N 521 LEU cc_start: 0.8685 (mt) cc_final: 0.8449 (mt) REVERT: N 525 ASN cc_start: 0.8420 (m-40) cc_final: 0.8054 (m-40) REVERT: N 572 LEU cc_start: 0.8103 (pp) cc_final: 0.7612 (tp) REVERT: N 645 THR cc_start: 0.8831 (p) cc_final: 0.8605 (p) REVERT: S 32 GLN cc_start: 0.6748 (pp30) cc_final: 0.6483 (pp30) REVERT: S 58 LYS cc_start: 0.4717 (mtmt) cc_final: 0.3418 (ttmt) REVERT: S 232 MET cc_start: 0.5943 (mmp) cc_final: 0.5463 (mmp) REVERT: S 477 VAL cc_start: 0.8634 (m) cc_final: 0.7682 (m) REVERT: P 42 LEU cc_start: 0.7977 (mt) cc_final: 0.7312 (tp) REVERT: P 173 MET cc_start: 0.7608 (ppp) cc_final: 0.7382 (ppp) REVERT: P 341 LEU cc_start: 0.7599 (mt) cc_final: 0.7274 (mt) REVERT: Q 210 CYS cc_start: 0.4403 (m) cc_final: 0.3896 (m) REVERT: Q 416 VAL cc_start: 0.7547 (t) cc_final: 0.7281 (t) REVERT: Q 420 ASN cc_start: 0.6224 (m-40) cc_final: 0.5903 (m110) REVERT: Q 434 TYR cc_start: 0.6603 (m-10) cc_final: 0.4931 (m-80) REVERT: U 247 ILE cc_start: 0.8565 (tp) cc_final: 0.8343 (tp) REVERT: O 78 VAL cc_start: 0.7911 (t) cc_final: 0.7521 (t) REVERT: O 132 GLU cc_start: 0.6644 (tp30) cc_final: 0.6415 (tp30) REVERT: O 294 MET cc_start: 0.3840 (mtt) cc_final: 0.3321 (mtt) REVERT: O 350 ILE cc_start: 0.8612 (mm) cc_final: 0.8392 (pt) outliers start: 2 outliers final: 1 residues processed: 916 average time/residue: 0.5123 time to fit residues: 770.0836 Evaluate side-chains 735 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 734 time to evaluate : 4.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 445 optimal weight: 7.9990 chunk 469 optimal weight: 5.9990 chunk 427 optimal weight: 30.0000 chunk 456 optimal weight: 9.9990 chunk 468 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 358 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 412 optimal weight: 9.9990 chunk 431 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 29 GLN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 204 HIS V 279 HIS V 291 ASN ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 ASN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN Z 156 HIS Z 166 ASN ** Z 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 361 HIS ** Z 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN N 305 ASN ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 900 ASN ** S 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 286 ASN ** P 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 366 ASN Q 54 GLN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 226 HIS ** Q 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 256 ASN O 107 GLN ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS O 282 GLN O 318 HIS O 343 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5407 moved from start: 0.9695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 41662 Z= 0.343 Angle : 0.825 13.461 56279 Z= 0.435 Chirality : 0.046 0.310 6447 Planarity : 0.005 0.060 7202 Dihedral : 5.863 47.739 5504 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.23 % Favored : 93.38 % Rotamer: Outliers : 0.04 % Allowed : 1.29 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5108 helix: -0.16 (0.08), residues: 3334 sheet: -1.10 (0.33), residues: 222 loop : -1.85 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP T 151 HIS 0.022 0.002 HIS P 425 PHE 0.058 0.003 PHE R 31 TYR 0.034 0.003 TYR R 140 ARG 0.009 0.001 ARG W 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 898 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 6 THR cc_start: 0.5765 (p) cc_final: 0.5543 (p) REVERT: W 76 LEU cc_start: 0.7866 (tt) cc_final: 0.7660 (tt) REVERT: W 137 VAL cc_start: 0.7093 (t) cc_final: 0.6794 (t) REVERT: W 167 GLU cc_start: 0.5118 (tt0) cc_final: 0.4594 (tt0) REVERT: V 34 LEU cc_start: 0.8773 (tp) cc_final: 0.8562 (tp) REVERT: V 95 LEU cc_start: 0.6443 (mt) cc_final: 0.6138 (mt) REVERT: V 118 LEU cc_start: 0.7928 (mt) cc_final: 0.7727 (mt) REVERT: V 157 ARG cc_start: 0.7028 (ttt180) cc_final: 0.6185 (tpp80) REVERT: V 196 TYR cc_start: 0.6709 (p90) cc_final: 0.6199 (p90) REVERT: V 212 MET cc_start: 0.6648 (ttp) cc_final: 0.6428 (ttp) REVERT: V 285 ASP cc_start: 0.5447 (t70) cc_final: 0.4752 (t0) REVERT: T 89 TYR cc_start: 0.3709 (m-80) cc_final: 0.3439 (m-80) REVERT: X 74 MET cc_start: 0.4462 (tpt) cc_final: 0.4232 (tpt) REVERT: X 125 MET cc_start: 0.6646 (tmm) cc_final: 0.6378 (tmm) REVERT: Y 27 LYS cc_start: 0.7171 (tttt) cc_final: 0.6865 (ttmt) REVERT: Z 9 GLN cc_start: 0.1835 (mm110) cc_final: 0.0663 (tp-100) REVERT: Z 103 TYR cc_start: 0.4948 (t80) cc_final: 0.4659 (t80) REVERT: Z 152 GLU cc_start: 0.4926 (mp0) cc_final: 0.4278 (mp0) REVERT: Z 375 ASP cc_start: 0.3714 (p0) cc_final: 0.3408 (p0) REVERT: Z 525 MET cc_start: 0.5351 (ptp) cc_final: 0.4926 (ptp) REVERT: Z 595 MET cc_start: 0.5386 (mtm) cc_final: 0.4787 (mtt) REVERT: Z 793 PHE cc_start: 0.0216 (m-10) cc_final: -0.0146 (m-10) REVERT: N 46 ILE cc_start: 0.3487 (mt) cc_final: 0.3221 (mt) REVERT: N 64 ILE cc_start: 0.5444 (mt) cc_final: 0.5194 (mt) REVERT: N 301 THR cc_start: 0.6773 (m) cc_final: 0.6350 (m) REVERT: N 457 SER cc_start: 0.9204 (p) cc_final: 0.8873 (t) REVERT: N 521 LEU cc_start: 0.8691 (mt) cc_final: 0.8423 (mt) REVERT: N 525 ASN cc_start: 0.8275 (m-40) cc_final: 0.7915 (m-40) REVERT: N 572 LEU cc_start: 0.8199 (pp) cc_final: 0.7797 (tp) REVERT: N 652 VAL cc_start: 0.8135 (t) cc_final: 0.7925 (t) REVERT: N 747 HIS cc_start: 0.7534 (m90) cc_final: 0.7214 (m-70) REVERT: S 58 LYS cc_start: 0.4539 (mtmt) cc_final: 0.3359 (ttmt) REVERT: S 273 PHE cc_start: 0.7555 (m-80) cc_final: 0.7144 (m-80) REVERT: S 421 TYR cc_start: 0.7389 (m-80) cc_final: 0.6643 (m-80) REVERT: P 421 GLU cc_start: 0.7699 (pm20) cc_final: 0.7392 (pm20) REVERT: Q 98 LYS cc_start: 0.7918 (tptp) cc_final: 0.7377 (tptp) REVERT: Q 99 THR cc_start: 0.7350 (p) cc_final: 0.7112 (p) REVERT: Q 210 CYS cc_start: 0.4220 (m) cc_final: 0.3730 (m) REVERT: Q 420 ASN cc_start: 0.6085 (m-40) cc_final: 0.5840 (m-40) REVERT: Q 434 TYR cc_start: 0.6758 (m-10) cc_final: 0.5137 (m-80) REVERT: R 197 MET cc_start: 0.6081 (ptp) cc_final: 0.5083 (ptp) REVERT: R 353 MET cc_start: 0.4201 (pmm) cc_final: 0.3168 (pmm) REVERT: U 12 PRO cc_start: 0.7889 (Cg_endo) cc_final: 0.7499 (Cg_exo) REVERT: U 73 ILE cc_start: 0.7157 (mt) cc_final: 0.6859 (mt) REVERT: U 229 LEU cc_start: 0.7849 (mm) cc_final: 0.7577 (mm) REVERT: U 245 ASP cc_start: 0.6625 (m-30) cc_final: 0.6049 (m-30) REVERT: U 247 ILE cc_start: 0.8631 (tp) cc_final: 0.8388 (tp) REVERT: U 268 LYS cc_start: 0.7504 (mmtm) cc_final: 0.7153 (mmtm) REVERT: O 32 PHE cc_start: 0.7103 (m-10) cc_final: 0.6817 (m-10) REVERT: O 132 GLU cc_start: 0.6728 (tp30) cc_final: 0.6394 (tp30) REVERT: O 294 MET cc_start: 0.3720 (mtt) cc_final: 0.3170 (mtt) REVERT: O 342 ASP cc_start: 0.3915 (t0) cc_final: 0.2826 (t0) REVERT: O 350 ILE cc_start: 0.8848 (mm) cc_final: 0.8481 (pt) outliers start: 2 outliers final: 0 residues processed: 899 average time/residue: 0.5219 time to fit residues: 772.7513 Evaluate side-chains 714 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 714 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 454 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 chunk 482 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 335 optimal weight: 9.9990 chunk 506 optimal weight: 6.9990 chunk 465 optimal weight: 9.9990 chunk 403 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 204 HIS ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 GLN T 112 ASN T 116 GLN ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 204 ASN Y 25 ASN ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 ASN ** Z 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 361 HIS ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN ** N 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 870 ASN N 878 GLN N 900 ASN S 91 ASN ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 278 ASN P 286 ASN P 289 ASN ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 HIS Q 147 GLN Q 150 GLN Q 226 HIS Q 253 ASN ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 GLN ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 256 ASN ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN O 282 GLN O 318 HIS O 343 GLN O 345 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5257 moved from start: 0.9771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41662 Z= 0.217 Angle : 0.712 12.862 56279 Z= 0.373 Chirality : 0.043 0.260 6447 Planarity : 0.004 0.067 7202 Dihedral : 5.500 41.106 5504 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.23 % Favored : 94.40 % Rotamer: Outliers : 0.07 % Allowed : 0.39 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.11), residues: 5108 helix: 0.14 (0.09), residues: 3337 sheet: -0.75 (0.34), residues: 209 loop : -1.86 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP O 38 HIS 0.021 0.002 HIS P 425 PHE 0.038 0.002 PHE N 682 TYR 0.033 0.002 TYR O 98 ARG 0.009 0.001 ARG S 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 903 time to evaluate : 5.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 76 LEU cc_start: 0.7597 (tt) cc_final: 0.7392 (tt) REVERT: W 137 VAL cc_start: 0.7052 (t) cc_final: 0.6788 (t) REVERT: W 167 GLU cc_start: 0.5095 (tt0) cc_final: 0.4709 (tt0) REVERT: V 157 ARG cc_start: 0.7104 (ttt180) cc_final: 0.6320 (tpp80) REVERT: V 158 LEU cc_start: 0.8155 (tp) cc_final: 0.7660 (tp) REVERT: T 89 TYR cc_start: 0.3105 (m-80) cc_final: 0.2875 (m-80) REVERT: X 125 MET cc_start: 0.6775 (tmm) cc_final: 0.6396 (tmm) REVERT: Y 27 LYS cc_start: 0.6972 (tttt) cc_final: 0.6738 (ttmt) REVERT: Z 9 GLN cc_start: 0.1911 (mm110) cc_final: 0.0761 (tp-100) REVERT: Z 152 GLU cc_start: 0.5078 (mp0) cc_final: 0.4563 (mp0) REVERT: Z 153 TYR cc_start: 0.1620 (p90) cc_final: -0.1063 (p90) REVERT: Z 403 ASN cc_start: 0.4288 (m-40) cc_final: 0.3930 (p0) REVERT: Z 525 MET cc_start: 0.5038 (ptp) cc_final: 0.4690 (ptp) REVERT: Z 595 MET cc_start: 0.5205 (mtm) cc_final: 0.4634 (mtt) REVERT: Z 793 PHE cc_start: 0.0908 (m-10) cc_final: 0.0596 (m-10) REVERT: N 46 ILE cc_start: 0.2958 (mt) cc_final: 0.2593 (mt) REVERT: N 166 ILE cc_start: 0.5579 (mm) cc_final: 0.5278 (mm) REVERT: N 301 THR cc_start: 0.6218 (m) cc_final: 0.5890 (m) REVERT: N 339 MET cc_start: 0.5115 (mmm) cc_final: 0.4617 (mmm) REVERT: N 450 ILE cc_start: 0.7808 (tp) cc_final: 0.7049 (tt) REVERT: N 457 SER cc_start: 0.9006 (p) cc_final: 0.8666 (t) REVERT: N 521 LEU cc_start: 0.8657 (mt) cc_final: 0.8366 (mt) REVERT: N 525 ASN cc_start: 0.8360 (m-40) cc_final: 0.8035 (m-40) REVERT: N 572 LEU cc_start: 0.8091 (pp) cc_final: 0.7708 (tp) REVERT: N 645 THR cc_start: 0.8768 (p) cc_final: 0.8550 (p) REVERT: N 682 PHE cc_start: 0.7064 (m-80) cc_final: 0.6862 (m-10) REVERT: N 747 HIS cc_start: 0.7564 (m90) cc_final: 0.7171 (m-70) REVERT: S 58 LYS cc_start: 0.5049 (mtmt) cc_final: 0.3590 (ttmt) REVERT: S 229 THR cc_start: 0.7453 (p) cc_final: 0.7138 (p) REVERT: S 273 PHE cc_start: 0.7321 (m-80) cc_final: 0.7046 (m-80) REVERT: P 341 LEU cc_start: 0.7731 (mt) cc_final: 0.7515 (mt) REVERT: P 356 TYR cc_start: 0.6192 (m-80) cc_final: 0.5857 (m-10) REVERT: P 380 ILE cc_start: 0.7754 (pt) cc_final: 0.7389 (mt) REVERT: Q 4 PRO cc_start: 0.4842 (Cg_exo) cc_final: 0.4580 (Cg_endo) REVERT: Q 98 LYS cc_start: 0.7935 (tptp) cc_final: 0.7278 (tptp) REVERT: Q 210 CYS cc_start: 0.4061 (m) cc_final: 0.3589 (m) REVERT: Q 420 ASN cc_start: 0.6233 (m-40) cc_final: 0.5946 (m-40) REVERT: Q 434 TYR cc_start: 0.6358 (m-10) cc_final: 0.4596 (m-80) REVERT: R 197 MET cc_start: 0.5467 (ptp) cc_final: 0.4163 (ptp) REVERT: R 269 LYS cc_start: 0.5898 (mttp) cc_final: 0.5607 (mttp) REVERT: R 353 MET cc_start: 0.3966 (pmm) cc_final: 0.2912 (pmm) REVERT: R 405 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6815 (mmtt) REVERT: U 1 MET cc_start: 0.5157 (mtm) cc_final: 0.4305 (mtm) REVERT: U 14 VAL cc_start: 0.7632 (t) cc_final: 0.7368 (t) REVERT: U 73 ILE cc_start: 0.6484 (mt) cc_final: 0.6219 (mt) REVERT: U 115 GLN cc_start: 0.6849 (mm110) cc_final: 0.6642 (mm-40) REVERT: U 229 LEU cc_start: 0.7867 (mm) cc_final: 0.7601 (mm) REVERT: U 245 ASP cc_start: 0.6575 (m-30) cc_final: 0.6001 (m-30) REVERT: U 247 ILE cc_start: 0.8599 (tp) cc_final: 0.8279 (tp) REVERT: O 294 MET cc_start: 0.3519 (mtt) cc_final: 0.2984 (mtt) REVERT: O 330 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6446 (ttp80) REVERT: O 350 ILE cc_start: 0.8706 (mm) cc_final: 0.8383 (pt) outliers start: 3 outliers final: 1 residues processed: 905 average time/residue: 0.5219 time to fit residues: 780.9682 Evaluate side-chains 721 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 720 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 247 optimal weight: 1.9990 chunk 320 optimal weight: 7.9990 chunk 429 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 371 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 403 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 414 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 29 GLN W 38 GLN ** V 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 204 HIS ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 ASN ** Z 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 361 HIS Z 378 GLN ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 GLN ** N 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 900 ASN ** S 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 278 ASN ** P 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 HIS ** Q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 226 HIS ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 142 GLN ** U 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 256 ASN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS O 282 GLN O 283 HIS O 343 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.154795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.129186 restraints weight = 170798.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.131560 restraints weight = 122940.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.132862 restraints weight = 90303.432| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.9918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41662 Z= 0.214 Angle : 0.705 14.036 56279 Z= 0.368 Chirality : 0.042 0.274 6447 Planarity : 0.004 0.067 7202 Dihedral : 5.470 48.268 5504 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.83 % Favored : 93.85 % Rotamer: Outliers : 0.09 % Allowed : 0.33 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5108 helix: 0.19 (0.09), residues: 3345 sheet: -0.82 (0.33), residues: 224 loop : -1.81 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP O 38 HIS 0.019 0.001 HIS P 425 PHE 0.037 0.002 PHE S 185 TYR 0.053 0.002 TYR R 252 ARG 0.006 0.001 ARG P 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12847.00 seconds wall clock time: 230 minutes 10.78 seconds (13810.78 seconds total)